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1. You should now have either the boat form or the twist boat form of cyclohexane The boat form is shown above Note If cleaning returns the model back to the chair form drag the CH group even farther above the seat of the chair than it was in step 3 and even closer to the back of the chair Then repeat the Clean step Rotate and view the model C Editing cyclohexane to make benzene In the following steps you learn how to edit bonds and to edit and delete atoms and so build benzene from cyclohexane Cerius Modeling Environment April1999 69 3 Tutorials 1 Delete the hydrogens from cyclohexane Find the two popups on the tool bar that currently read Atom Change the second of these to El for element Both of these popups control the selection rules for atom picking Setting the second popup to El means that all atoms of the same element type are selected when one atom of that type is picked Select one hydrogen atom All hydrogens appear selected in the model window Double click the Delete Atom icon in the Sketcher control panel All the hydrogens in the model are deleted This delete procedure has illustrated the alternative way of applying the Sketcher icons double clicking on an icon carries out its action on all selected atoms 2 Make the double bonds Change the second selection rule popup back to its default Atom setting Also highlight the
2. 0000000 05 344 Manipulating text 0 cece eee eee 347 Table and command operations 348 Recalculating table values 1 0 cece eee 349 Cerius Modeling Environment April 1999 xi Models in tables 0 0 cee Copying models into columns 00005 Setting up calculations on models Saving tables containing models Grouping table information sssr rnn eee ae Creating a named group 6 e cece eee eee Editing a group definition 0000 Selecting named groups 6 66 eee eee eee Deleting a group definition 0005 Searching for information ina table 00 Viewing subsets of a table naaa 6 c eee eee Viewing named groupS 6 6 06 cece eee eae Viewing search results 060 c cece ees Sorting table information 06 0c eee eens Graphing table information 0 000s eee Exporting table information 0 000 eee 12 Working with Isosurfaces Analyzing 3D grid properties 0 6 0 c eee eee Mapping a property onto a surface Editing and displaying slices 004 13 Scripts and Licensing Command logging and scripting 00000 Recording commands sasssa assanar arrn Command tracing sss sasssa eee Controlling Cerius from a Ta DEE E EEEE Playing back scripts and log files 0 Starting Cerius with a comm
3. Review In this tutorial you learned how to 2 Display multiple models using the Model Manager I Remove and clear models from the Model Manager list I Create a new model space 92 Cerius Modeling Environment April 1999 Related material Managing and Modifying Graphs 11 Copy atoms between model spaces 1 Duplicate selected atoms 1 Move one model fragment relative to another 1 Measure model geometry d Generate a PostScript image from the model window Now you may want to proceed to the next tutorial Managing and Modifying Graphs The model manager is discussed in detail in the Cerius Modeling Environment If you haven t already done so you may want to read the introductory tutorial in Chapter 2 of that book Other sections of that book that relate to the activities in this lesson include Using the main control panel in Chapter 2 Controls and control panels in Chapter 2 Basic building in Chapter 4 Printing models and graphs in Chapter 7 Managing and Modifying Graphs This chapter contains a tutorial exercise about graphs in Cerius It introduces the basics of viewing modifying saving and loading graphs that are created by Cerius This chapter is divided into four parts Before you begin provides some introductory and background information Step by step tutorial gives you specific instructions to follow Review summarizes the exercise by giving a checklist of the
4. Key Operation Action click Select only one model Controlling model visibility and the display mode drag Select only a range of models double click Select all models lt Shift gt click Select from the last selection through the model clicked upon lt Ctri gt click Select deselect the clicked model no change to other selections lt Ctr gt drag Selecta range of models no change to other selections lt td gt double click Deselect all models Mhe check mark indicates which mouse button to press Graph window Table 30 Manipulating graph in graph window with mouse Button M SINSINIS v v Key Operation Action lt Ctr gt click Identify coordinates and data pointsin graph drag horizontally Scroll along the x axis drag vertically Scroll along the y axis lt Shift gt drag Zoom in or out on graph lt Alt gt drag Zoom in on area within the dragged out rectangle Changing graph axes and scale drag Zoom in or out on graph Changing graph axes and scale Mhe check mark indicates which mouse button to press Cerius Modeling Environment April 1999 409 C Mouse and Keyboard Actions Model window Table 31 Manipulating model in model window with mouse Button Vv S SISISISIS SISISIS lt lt Vv lt Key lt shift gt lt hift gt lt tr gt lt shift gt
5. Review summarizes the exercise in a checklist of the skills you ve learned and suggests what to do next and points you to MSI documentation that provides more detailed information about the functions introduced in the tutorial exercise 76 Cerius Modeling Environment April 1999 Managing Modelsand More Before you begin Summary of tutorial To complete this tutorial you need a licensed copy of Cerius and a directory into which you can save the files that you create during the tutorial Before you start this tutorial lesson page 50 you should have read or be familiar with the contents of Basic GUI Functions and have done the tutorial exercises in Using the 3D Sketcher In this tutorial you load in and use the models that you created in Using the 3D Sketcher The tutorial is divided into five short exercises A Using the model manager B Making picric acid from phenol transferring data between model spaces C Building a model of indigo D Measuring the indigo model E Generating hard copy Step by step tutorial This section includes a series of short progressive exercises describ ing various aspects of the Cerius Visualizer model management measuring models and creating Postscript images for printing You will use the controls in the model manager to complete the steps of Cerius Modeling Environment April1999 77 3 Tutorials this tutorial The components of the model manager are
6. Additional information Please see the on screen help for details on the functioning of each control in the Viewing Dials control panel Mouse functions and keyboard shortcuts are summarized in Mouse and Keyboard Actions 232 Cerius Modeling Environment April 1999 Rotating models Manual rotation Tip Changing the default mouse rotation action Large rotations Moving models on the screen To interactively change the viewing angle of models place the cur sor in the model window and then To rotate the models about the x axis press the right mouse but ton and move the mouse vertically in the central area of the model window To rotate the models about the y axis press the right mouse but ton and move the mouse horizontally in the central area of the model window To rotate the models about the y axis press the right mouse but ton and move the mouse horizontally or vertically near an edge of the model window The default mouse behavior described here can be altered by changing the mouse rotation action from normal to continuous or rock see Changing the default mouse rotation action To change the default way in which mouse driven rotations behave select the View Options menu item to access the View Options control panel Choose the desired function under Mouse Rotate Action The available modes are NORMAL As described under Manual rotation CONTINUOUS As described under Manual rotati
7. For isotropic factors the default format is U iso FOr anisotropic the default format is Uj Cerius Modeling Environment April 1999 187 5 Building Models Table 3 Forms of temperature factor terms Form Relationship to H or x2 Scattering amplitude multiplied by gt 87 U o Sin 0 Viso Uso x 42 Tak B sin20 2152 pa NSO e Biso Biso 8T x 72 Tak xy Taiki l U A HA Uj U j Jij 27y hea Unyk2b Uz c 2U yhka b 2U5 kIb c 2U hla c e i Tiy By B 8n7 AHA yj lB nat B k b Baal2c 2B hka b 2B klb c 2B hla c 41 4 22 33 faith 23 Pe Ae By 2 Bi ae ne Birt Bank Bagi 2B ghk 2By 3k 2B 3hl 2n A1HA jjla al la b c a b c etc For the factor of two on the crosstermsis included in the term forsome structure file formats please see File Formats for more details Typical applications affected by temperature factors are X ray eletron and neutron diffraction calculations see separate docu mentation and the display of thermal ellipsoids Thermal ellip soids Specifying temperature factors Temperature factors can be specified when you add new atoms Select the Build Add Atom menu item to access the Add Atom control panel In this control panel click the Temperature Fac tors pushbutton to access the Added Atom Temperature Factors control panel 188
8. Managing and editing tables Why read this section If you run calculations in any application modules that output tables you need to know at least how to load save and close 316 Cerius Modeling Environment April 1999 Finding information Related information You should already know Concepts Managing and editing tables tables and how to specify the current table in the table manager window The other information in this section is useful if you want to create tables by hand or from an imported text file to edit any table or to move around in tables that are larger than the current table display area in the table window This section includes information on Creating a new table Loading and reloading tables Importing an ASCII text file into a new table Specifying the current table Entering values and editing individual cells Copying moving and clearing information Inserting and deleting entire rows or columns Table expansion and cursor control Saving a table Closing a table Table style and format is presented under Table style and display How to access the Tables module is described under Accessing the tools How to display a table window is shown under Accessing the tools Table management tasks are those that apply to tables as a whole rather than to the rows and columns of a table In the Cerius Tables module table management functions are accomplished in the table manager section of the Tabl
9. Object name Binary model operators Table 19 take two arguments The first argument must evaluate to a cell of type molecular The operators return null if anything else is specified Several of these operators use atom names to specify the second argument Atom names can be separated by commas or hyphens if more than one atom name is required Hyphens work exactly like columns in these table expressions hyphens do not indicate ranges of atoms The following examples assume that column one contains molec ular type data distance col Structure CA CB charge col 1 CA bonds col 1 Some expressions involving models can be complicated to set up manually Provided you have the desired model present in the model window Cerius can calculate certain properties and automatically insert them in a table column for details see Setting up calculations on models Cerius Modeling Environment April 1999 345 11 Working with Tables Table 19 Binary model operators in Cerius table expressions Operator Retums angle number anglebyname number charge number chargebyname number distance number distancebyname number ecount number exact number smol number sss number Description Bond angle in degrees atoms referenced using a named triple Usage angle col structure C1 C2 C3 Bond angle in degrees atoms referenced using a user assigned name Usage angle col structure CA CB CC P
10. Tip Cerius and independent processes To always run an application module externally under the conditions you set with the Process Management control panel you need to save the current session Saving the current session Otherwise your settings are saved only for the current Cerius session Some application modules for example those on the QUANTUM cards are actually used only to set up and act as interfaces to cal Cerius Modeling Environment April 1999 385 13 Scripts and Licensing Accessing the tools Specifying processing conditions Tip culations that are run by essentially separate programs that are independent of the Cerius interface Such modules offer their own job control options that affect the separate usually computa tionally intensive program These controls are accessed from the application module itself and are documented in the user guide for the relevant module The Process Management control panel affects only those pro cesses that are under the direct control of the Cerius interface not independent processes that are spawned by applications such as the quantum modules For example the MOPAC interface application control panels etc is controlled by the Process Management control panel but the MOPAC program itself the calculation job is managed by MOPAC Job Control control panel Select the Utilities External Processes menu item in the main Visualizer control panel to
11. YLABEL string Text for the Y axis label TITLE lines The number of title lines on records to follow SCALES ON OFF Axis box numbering the default is ON KEY ON OFF The default is ON PLOT name version An x y data set ODB within the file These may occur any number of times for different data sets within the ODB Sequenced in plotting order that is in reverse precedence gt GRAPH 2D METHOD name version name and version Unique to this graph These are very similar to data set name and version number 432 Cerius Modeling Environment April 1999 Descriptors Gallery ODB Initiation record Descriptors Grf SYSTEM POLAR CARTESIAN XMIN ordinate angle in degrees XMAX ordinate angle in degrees YMIN ordinate Not needed in polar system YMAX ordinate radius AXES RECTANGULAR OBLIQUE Cartesian system only The default is OBLIQUE XYANGLE angle in radians Cartesian system only Angle between axes ASPECT default is 1 0 XLABEL YLABEL TITLE SCALES aspect ratio Cartesian system only y x The string Text for the x axis label string Text for the y axis label lines The number of title lines on records to follow ON OFF Axis box numbering The default is ON KEY ON OFF The default is ON PLOT name version A 2D dataset ODB within the file These may oc
12. d i n g F e r erB g KER Oo 1 5 2 0 2 5 3 0 3 5 4 0 5 Pressure Pa x10 4 SORPTION Loading Plot vi 102 Cerius Modeling Environment April 1999 C Scaling graphs Managing and Modifying Graphs 2 Editing more than one dataset at a time On the Graph Manager control panel select all the Sorption data sets for both Display and Edit Return to the Plotting Attributes control panel Notice how the Style and Color popups show the gt symbol and the Y Offset and Label text boxes are blank This is because the attributes are not the same for all of the data sets The 01 and 03 data sets are in point style and the 02 is in line Furthermore the colors of all three are differ ent and the key labels and Y offsets also differ Set the Y Offset to 0 zero Experiment with the Style popup set it to Histogram to Delta to Point and finally to Line You could also use the Color popup to set all the lines to the same color or the Label text box to make the labels the same for all of the datasets but these would not be very useful Close the Plotting Attributes control panel In the following steps you learn four ways to alter the scale of a graph Using the scaling text boxes Cerius Modeling Environment April 1999 103 3 Tutorials Using the scroll and zoom buttons Using the mouse Using the Axis Scaling popup Use the text b
13. gt mkdir tutorialSession 212 Cerius Modeling Environment April 1999 Saving the current session What is saved as a session Related information Working with C erius sessions Select the File Save Session menu item from the main control panel s menu bar to access the Save Session control panel This control panel is used to save the current session Use the file selector controls in the Save Session control panel to move through the file system to the directory in which you want to save the current model Newly created directories appear in the file selector list box when the appropriate parent directory is opened or reopened with the file selector controls or when the con trol panel is opened After selecting the appropriate directory specify a name for the session file by typing that name in the file name text entry box then press lt Enter gt or click the SAVE button A warning helps prevent you from accidentally overwriting exist ing session and model files You may choose and enter an existing filename if you want to overwrite an existing session file A saved session consists of a session file mss file extension and a set of standard MSI format structure model files When you save a session one model is written in the specified directory for each occupied model space The session file contains application preferences customizations any cross model linkages and refer ences to the saved structu
14. Accessing the tools Select the Edit Selection menu item to access the Atom Selec tion control panel Click the Custom Selection pushbutton to access the Customized Atom Selection control panel Cerius Modeling Environment April 1999 163 5 Building Models Setting multiple and cus tomized criteria Finding atom information Additional information To set up customized selection criteria you can pick properties from the popups in the Customized Atom Selection control panel and enter additional subcriteria in the associated entry boxes Wildcards are allowed in the subcriteria Also multiple subcriteria may be entered into an entry box separate the individual subcri teria with a colon For example you can select all atoms whose name starts with c which have a desired range of charge values and are located within residues of a certain type For maximum flexibility you can also use raw object reference lan guage to select atoms Please see the on screen help for the syntax To enter information into the subcriteria boxes you of course need to know what an atom s properties are You can query atom properties by shift clicking the atom with the right mouse button Tip This displays a temporary message box and also prints to the text window You can also choose to have brief information on atom properties sent to the text window whenever you click an atom To do this select the Utilities Customize Env
15. Bonds as sticks Understanding the display Specifying stick style Display styles can be applied to entire models when all or no atoms are selected or to selected atoms within one or more mod els Different display styles may be used for different parts of a model This section includes information on displaying Bonds as sticks Bond order display Bonds as cylinders Lone atoms Atoms as balls Ball and stick models Cations as polyhedra Thermal ellipsoids A tutorial example of changing model display styles is found under Changing the display style Please see the on screen help for details on the functioning of each control mentioned in this section The default is to display bonds as single double or triple lines Atoms are not specifically shown but are present at the ends of bonds The bond colors represent the element types of the atoms at each end Pe To reset stick display style you can Set the display style popup on the toolbar to STICK Cerius Modeling Environment April 1999 249 8 Viewing and Displaying Models Select the View Display Attributes menu item to access the Display Attributes control panel Set the Style popup to STICK Bond order display Understanding the display Multiple bonds can be shown as a set of parallel lines representing the bond order Partial double bonds in 6 membered ring systems can be represented as both displayed and stored with the model as Kekule o
16. Creating a named group from search results Duplicating an existing group You can create a named group from a selection of rows or columns by saving the results of a search Searching for information ina table as a group or by duplicating an existing group To create a named group from selected rows and or columns you need to access the Table Groups control panel Click the GROUPS tool in the table manager tool bar or Select the Data Groups menu item from the TABLES card Assure that the Selection tool is selected enter a name in the Group Name entry box then click the CREATE pushbutton All currently selected rows and or columns are included in the newly defined group The columns and or rows need not be contigu ous First defining a table as a group could be a convenient way of selecting or displaying the original table after you have added col umns or rows to that table To create a group from the entire table access the Table Groups control panel as under Creating a named group from a selection Select the Entire Table tool enter a name in the Group Name entry box then click the CREATE pushbutton To create a named group from the results of a search you can spec ify that the search results be output as a group Before starting the search Searching for information in a table check the Save Results check box in the Find Cells control panel and enter a name in the associated Group entry box After the
17. For Cerius graphs loading the graph also loads its included data sets 296 Cerius Modeling Environment April 1999 Additional information File formats Displaying and editing graphs However since Insight graphs contain multiple data sets you need to first select the graph and then choose the desired types of data to be plotted Then click the PLOT pushbutton to load the graph and the desired data sets Please see the on screen help for details on the functioning of each control in the Load Graphs and Import TBL File control panels Because all Cerius graphs are saved in the grf format most graphs loaded in are also in this format However the Cerius graph system recognizes and correctly loads graphs in the xy and con formats used by CERIUS prior to version 3 1 Cerius can also read in graphs that were saved in the Insight II program s tbl format Cerius tbl files are not the same format as Insight tbl files Cerius recognizes graph files according to their format so it is not strictly necessary to save them with the standard filename exten sions However itis generally less confusing and more convenient to do so For detailed information about Cerius file formats please see File Formats Insight files are described in separate file formats docu mentation Displaying and editing graphs Why read this section Finding information When a graph is output by an application it automati
18. 3 Tutorials Note If you specify a gallery size that is too small for the number of graphs graphs will disappear from the Gallery window To redisplay a lost graph set the gallery size large enough for all the graphs and then select again the missing graphs on the Graph Chooser list box of the Gallery Manager control panel Set the Label Graphs check box to on Note the appearance of the graph labels in the graph window Uncheck the Emix Fit v1 and the Thermodynamics v1 graphs on the Graph Chooser list box to leave only the Sorption Loading Plot on display in the graph window Be sure that the Edit box for the Sorption Loading Plot graph is toggled on B Using the Graph Manager and setting plotting attributes Now that you ve looked at the Gallery Manager and used it to edit the layout of graphs in the graph window you learn how to edit the graphs themselves using the Graph Manager 1 Open the Graph Manager Open the Graph Manager control panel by clicking the Graph Manager button at the bottom of the Gallery Man ager control panel Alternatively open the control panel by choosing Graph gt Manager from the Graphs card The Graph Manager control panel has a Data Set Chooser list box that parallels the Graph Chooser browser box in the Gallery Manager In the Data Set Chooser are listed the data sets of all three of the loaded graphs but only the data sets currently displayed on the Sorp
19. Tip The table manager has several control panels that can be open at the same time Each control panel keeps track of the current table and updates its display to reflect the current conditions for the active table When using control panels accessed from the Table Manager win dow or the TABLES card you need to be sure of which table the panel is attached to that is which table is affected by using the tools in the control panel Note that the table window includes two tabular displays that con tain a current cell the current table in the main table section and the list of tables in the table manager section Therefore When you are working in a control panel make sure its Table entry box contains main_table Otherwise changes you make may be applied to the list of tables rather than the current table In addition you may have several table windows open simulta neously which may be associated with different Cerius modules If so control panels need to be attached to both the correct table and the correct table window many table related control panels can operate on any displayed table even if the Table Manager window does not know about that table Therefore If you have several table windows open it is good practice to click once in the table window with which you are working before using tools in a control panel This assures that the control panel s Table entry box refers to the correct current table
20. can be used to cancel one or a series of previous commands for many types of operations The UNDO button is greyed out when there is nothing to cancel Helo Checking the Guide check box gives you on screen help in the upper left corner of the model window on the Annotation control panel functions Additional information Please see the on screen help for details on the functioning of each control in the Annotation control panel Model display style Why read this section You can change the model display to suit your needs For example you may want to display molecules in traditional stick style or with ellipsoids representing thermal movements of atoms you may want to emphasize some atoms or you may want to view a cross section of a model Finding information This section includes information on Atom and bond display styles Structure traces Cross sections of models Apparent depth effects Related information Labeling atoms according to various properties is discussed under Labels Setting the graphical quality and screen resolution is dis cussed under Resolution and graphical quality You can also enhance model displays by for example coloring atoms according to various properties Model display colors or add ing Connolly Model surfaces or other surfaces 248 Cerius Modeling Environment April 1999 Model display style Atom and bond display styles Finding information Example Additional information
21. color mapping 6 6 c cece 274 Creating and editing a binary property color map275 Cree and editing a continuous property color map 27 Editing a property color map 278 Surfaces style and transparency 0 0 eee 278 Lighting control 6 eee 279 Adjusting global light settings 00 282 Defining discrete light sources 0000005 283 Color and components 1 0 0 0 0c eee eae 283 Directional lights 0 0 cece eee eee 284 Positional lights 6 0 6 eee eee ee eae 285 Spotlights ies saen an aa a enami ee eee es 286 Light attenuation 0 6 eee eee 287 Rendering and ray tracing 1 1 6 0 cece eee eee 287 StereO VIEWING eee eee 289 10 Working with Graphs 291 Creating graphs nnsa giaa A eee 293 x Cerius Modeling Environment April 1999 Starting anew empty graph 2 eee eee 294 Specifying the type of graph 0000000 294 Selecting Gata i plot is 3 Era t Ai a Taa Na Aaa AAGA 295 Loading graphs 6 cece cee 296 Displaying and editing graphs n ssaa saaana nnn 297 keine and dis Taing graphs si 1 eee eee 298 Selecting which data sets to display and edit 299 Labeling and annotating graphs 0 299 Changing graph axes and scale 0000005 301 Changing plotting style and color 303 Managing elas se deca at al Same he dessa Save shel Goce ae A 305 Controlling default display format
22. fullerene The Fuse tool on the Sketcher control panel can be used in several ways To fuse two fragments at one point select the Fuse tool then pick an atom in each fragment Click the second atom again to perform the fusion The first atom picked is deleted and the rest of the fragment is bonded to the second atom To fuse several atom pairs simultaneously Select the Fuse tool and pick each pair in succession Then click the last atom a second time or 156 Ceru Modeling Environment April 1999 Connecting fragments Tip Basic building While in selection mode select all the atom pairs to be fused Selecting atoms and groups of atoms then double click the Fuse tool Connecting two fragments means to join them by a bond deleting only hydrogens as necessary For example two benzenes could be connected to form biphenyl or connected twice to form biphe nylene The Connect tool on the Sketcher control panel can be used in sev eral ways To connect two fragments by a single bond select the Connect tool then pick each of the two atoms to be connected by a bond The fragments become oriented so as to give a reasonable bond length and orientation and extra hydrogens are deleted as appropriate To place a bond between two atoms in the same model select the Connect tool then pick each of the two atoms You can also select the two atoms first Selecting atoms and groups of atoms and then double c
23. lt Shift gt lt C ti gt lt Shift gt lt A It gt lt tr gt lt Cti gt lt Alt gt lt Shift gt lt Shift gt lt C t gt lt Shift gt lt C ti gt lt Shift gt lt C ti gt lt Shift gt lt Alt gt lt Cti gt lt Ctri gt lt Ctri gt Operation click drag click drag click drag drag drag drag drag drag drag honzontally drag vertically drag nearedge click drag honzontally drag vertically drag nearedge drag drag honzontally drag vertically drag nearedge drag Action Select an atom click empty spot to deselect all atoms Select atoms enclosed by dragged out rectangle Select or unselect additional atom Selecting and dese lecting individual atoms Select more atomsenclosed by dragged out rectangle Make a model current Specifying the current model Translate all models in xy plane Translating models Change magnification of model view Changing the view magnification Translate current model in xy plane Translating the cur rent model Change perspective angle Superimposing models Translate selected atomsasgroup in xy plane Translating and rotating atoms Translate selected atomsasa group along zaxis Rotate all models about y axis Rotating models Rotate all models about x axis Rotate all models about z axis Obtain information about atom properties Tip Rotate current model about y axis Rotating the current model Rotate current model about x ax
24. occupancy the atom name and temperature factors Specifying temperature factors see the on screen help for details Hybridiza tion is also discussed under Changing the hybridization and adjusting the valence the hybridization popup in the Add Atom control panel functions the same as in the Sketcher control panel After setting all desired parameters click the ADD ATOM action button to place the atom in the model window The most recently added atom can be deleted by clicking the UNDO button Adding templates groups of atoms Note Selecting templates The efficiency of the building process can often be improved by adding groups of atoms templates rather than single atoms You may start sketching a new model by placing a template in the model window or you can add templates to an existing model This section refers to using the Sketcher control panel The 3D Sketcher unless otherwise indicated The current template the one that is used if you click in the model window while the template tool is active is printed on the Sketcher control panel just to the right of the template tool for example phenyl To use a different template click the Templates pushbutton to the right of the template tool This causes the Sketcher Template control panel to appear This control panel contains a file browser that allows you to navigate among directories and load selected files that contain templates 154 Cer
25. set the pasted in information by making some cell other than the first one in row 5 current and not selecting the entire row It makes no difference if the target region is larger than the region contained in the clipboard The pasted in material either if it is from one cell replaces the contents of the current cell or if it is a row or column is inserted into the current table displacing the selected area down or to the right see Inserting and deleting entire rows or columns for information on inserting columns and rows To clear the values in the selected row s or column s or of the cur rent cell clearing does not remove mathematical expressions see Deleting expressions Click the CLEAR CELLS tool in the current table tool bar or Select the Edit Clear menu item from the TABLES card You can cut or clear the contents of rows columns or cells Moving cutting one or more cells and Clearing one or more cells and you can delete entire rows or columns Deleting columns and rows The dif ferences between these superficially similar operations are Clearing removes the information from the cell s and leaves the empty cells in the current table Cutting removes the information from the cell s places the information in the clipboard and either leaves the empty cell in the table if only the current cell was cut or removes the now empty cells from the current table if entire rows or columns were cut
26. 100 Cerius Modeling Environment April 1999 Managing and Modifying Graphs tion Loading Plot are checked Uncheck the Display button for the Sorption Loading Data 01 data set in the Data set Chooser list box to leave the Sorption Loading Data 02 and the Sorption Loading Data 03 data sets on display in the graph window Set the check boxes in the Edit column so that the Sorption Loading Data 02 data set can be edited but the Sorption Loading Data 03 data set cannot be The top portion of your Data Set Chooser should look like this Data Set Chooser Display Name Edit SORPTION Loading Data Ol vi WA SORPTION Loading Data 02 v1 P WA SORPTION Loading Data 03 v1 o ABTT v1 Click the Plotting Attributes button at the base of the Graph Manager control panel to open the Plotting Attributes control panel Change the Style popup currently reading Point to Line Observe that the data plot style changes from points to a line Use the Color popup currently reading YEL to change the line color to light green LGR Cerus Modeling Environment April 1999 101 3 Tutorials Edit the Label text box Observe that the text for the green line is modified Edit the Y Offset text box for example change it to 30 Observe the Y shift in the data plotted Edited label box for 233K 237K CERLUS Loading curve 30 Nitrogen in 5A 70 L o
27. 150 Cerius Modeling Environment April 1999 Basic building Some items in the Edit menu may provide quicker action than equivalent tools in the Sketcher control panel especially if the Sketcher control panel is not open and you need to make only a few changes Adding atoms and bonds The simplest procedure for building the basic structure of a model is to draw in the model window manually placing atoms con nected by single bonds at desired positions see Adding atoms and single bonds The model is then generally edited and finally its conformation is optimized Refining the conformation Precise posi tioning of atoms as they are added is also possible Precise position ing of atoms during building Note This section refers to using the Sketcher control panel The 3D Sketcher unless otherwise indicated Selecting the element type The sketching element type is listed in a text entry box to the right of the Sketch with tool FM Sketch with E You can change the sketching element type if needed in any of several ways Click this entry box and enter an element name in it Choose an element from the popup immediately to the right of this text entry box This popup lists several commonly used ele ments Select the periodic table tool to the far right of this text entry box When the Periodic Table window appears select the desired element Changing the element type automatically activates the Sketc
28. 180000 208 Cerius Modeling Environment April 1999 Saving model structure files Saving model structure files Why read this section Finding information Related information You should already know This section tells you how to save one or more models that are in your current Cerius session to store them on disk You will prob ably want to save models that you have built or modified and may want to use again You should save your model before running any calculation or performing other activities that might change its conformation if the original conformation of your model is impor tant This section includes information on Saving individual models Saving all models Building models is explained in Building Models and demonstrated in Introducing Cerius2 Loading models is discussed under Loading model structure files File formats are presented in File Formats The basics of starting Cerius and using its interface are demon strated in Introducing Cerius2 and described in The Cerius2 Interface Use of the file selection list box and other file selector controls to navigate the directory structure is presented in detail under Find ing model file s How to make a model be the current one is described under Basic model management tasks Saving individual models Making custom directories You may want to create your own directories or subdirectories in which to save models For example you may want t
29. Please see the on screen help for details on the functioning of each control in the control panels mentioned in this section Cerius Modeling Environment April 1999 277 9 Enhancing Model Display Editing a property colormap Accessing the tools Selecting the color map Editing the color map Additional information Select the Utilities Customize Color Mappings menu item from the main Visualizer control panel to access the Edit Color Mappings control panel Alternatively if you have the Color Selected Objects control panel open Accessing the tools you can click its Edit Mappings pushbutton to access the Edit Color Mappings control panel Choose the name of the map you want to edit from the Mapping popup Its current defining parameters appear in the control panel If you saved a custom color map during some earlier Cerius ses sion Saving a color map you have to load that session to access that color map see Loading a previously saved session Edit the map definitions by the same procedure as used in creating a color map Property color mapping You can also use the Edit Color Mappings control panel to delete or rename a color map Please see the on screen help for details on the functioning of each control in the Edit Color Mappings control panel Surfac es style and transparency You should already know Accessing the tools Setting the transparency style Various Cerius application
30. Tip ments include chemically real elements mixture elements and dummy elements Select the Build Element Defaults menu item to access the Edit Elements control panel Changing element defaults changes the properties for atoms of that element type that already exist in the model as well as for all atoms added to models later in the current Cerius session Among other properties you can for example change The van der Waals radius that is used in producing BALL dis plays Atom and bond display styles of atoms The atomic radius which is used by the clean function Refining the conformation The color used to display an element Please see the on screen help for details on the functioning of each control in the Edit Elements control panel Mixture elements are special Cerius elements with atomic sym bols T TT M and MM whose properties you can specify as pro portions of those of up to eight real elements Such a mixture can be useful for example in studying disordered structures Introduc ing substitutional disorder Mixture elements are defined using the Element Mixtures control panel which you access by clicking the Mixtures pushbutton on the Edit Elements control panel You can also examine the compo sitions of predefined mixture elements with this control panel Cerius also allows you to use predefined dummy atoms These nonstandard elements as well as the mixture e
31. Using saved sessions as preferences settings erences You should already The basics of starting Cerius and using its interface are demon know strated in Introducing Cerius2 and described in The Cerius2 Interface Cerius Modeling Environment April 1999 389 14 Customizing the Interface Interface configuration Finding information Related information Visualizer customization options enable you to change various aspects of the Cerius graphical interface to suit your unique requirements This section includes information on Deck of cards menu configuration Control panel management Setting other Cerius preferences and performing certain functions automatically are covered under Working with Cerius2 sessions and Controlling Cerius2 from scripts See the following section Interface look and feel for information on changing control panel colors and some aspects of how Cerius runs Deck of cards menu configuration Accessing the tools Creating and renaming card decks Cerius enables you to change the configuration of the deck of cards menus You can Add cards to or remove cards from existing decks Change the order of cards in existing decks Create new decks and rename or remove others Save your deck configuration for future Cerius sessions Select the Utilities Customize Menu Deck menu item in the main Visualizer control panel to access the Customize Menu Deck control p
32. Utilities Access to Visualizer utilities which enable you to control record and play back Cerius sessions customize var ious aspects of the Cerius modeling environment and access and control external applications See Customizing the Interface and Scripts and Licensing 134 Cerius Modeling Environment April 1999 Using the main control panel Help Access to on screen help on the basics of the Cerius modeling environment and to some prerecorded demonstra tions Simply select the topic that you are interested in See also On screen help Keyboard shortcuts The functions of several pulldown menu items can also be carried out by using keyboard shortcuts generally lt Alt gt key combina tions when the cursor is in the model window Relevant key com bination are shown beside the item on the pulldown menu itself See also Keyboard shortcuts The toolbar The toolbar is located just below the menu bar in the main control panel Model viewing contols Atom selection contols Cascade contol panels Close all contol panels Menu card search t ETET t Types of controls in the toolbar Some controls on the toolbar duplicate functions of control panels relating to model viewing and selection others provide unique functionality Model viewing controls Use these controls to change the model s display style add change or remove labels and reset the position of the mo
33. and potentials are scalar functions that are defined in the continuous 3D space surrounding the model In practice they are evaluated on a fine grid of points that completely encompass the model This produces a large amount of information which is typically visual ized as an isosurface that is the constant value points surround ing the model are connected so as to form a surface The data can also be visualized as slices showing the values of the function on a 2D plane cutting through the model The Isosurfaces feature can read both grd and mbk file formats For detailed information about Cerius file formats please see File Formats Insight files are described in separate file formats docu mentation 370 Cerius Modeling Environment April 1999 Finding your surfacing files Surface specification and display Additional information Analyzing 3D grid properties To display the orbitals electron density or potential for your model as a surface or to change the display of an existing surface use the Isosurfaces control panel which is accessed by selecting the Surfaces menu item on the ISOSURFACES card If you want to display a currently undisplayed surface use the Files pushbutton to access the Isosurfacing Files control panel Select the desired grd or mbk file and click the LOAD button You can use the browser popup to access directories other than the cur rent one Once you have a surfacing file loaded and
34. and then choose the Exit button on the Exit Option dialog box Checklist review What next In this tutorial you learned how to m m m m m m m Load and save graph files Display graphs using the Gallery Manager Display data sets using the Graph Manager Alter the data plot style and color Specify a Y offset value for data sets Edit text for graph titles axes and keys Use the Expert Functions to selectively remove graphs and to control version overwrites In this tutorial exercise you have encountered only the xy linear graph Many Cerius modules also create 2D cartesian and polar graphs These graphs can be manipulated loaded saved modified in much the same way as the xy graphs When a polar or cartesian 116 Cerius Modeling Environment April 1999 Basic Molecular Simulation Minimization amp Dynamics contour graph is selected for editing the appearance of the Graph Scaling and Plotting Attributes control panels are automatically altered to show the special controls you need to modify 2D plots You may now want to run one of the Cerius example files that cre ates a 2D graph and practice scaling it and modifying its plot attributes For more information about 2D plots see the Graphs chapter of the Cerius Modeling Environment These are some of logfiles that generate 2D plots ANL_exafs_SiAs log ANL_hrtem_particle log ANL_gsas_inorganic log QM_mopac_SN2 log POL_diff_crys log
35. control in the Import Table control panel Specifying the current table Making a table current To edit format or perform other tasks that work on the contents of one table you need to select the desired table to make it current The contents of the current table are displayed in the upper section of the table window To specify a table as current click any cell in its row or its row heading in the list of tables that appears in the lower table man ager section of the table window Entering values and editing individual cells Understanding cell values You can generally override table column and row wide default types and formats values for any individual cell However you cannot override the data type for strongly typed cells see Assigning data types 320 Cerius Modeling Environment April 1999 Related information Selecting a cell Editing cell contents Entering your changes Managing and editing tables You can enter or change values only in the current cell The current cell is highlighted with a rectangle its contents appear in the cell edit window and the cell s location and additional information about its contents appear in the current cell information window for illustration see Accessing the tools The additional information consists of The word Derived if the value of the current cell is derived from a calculation see Values and mathematical expressions The words R
36. how to specify the current model see Specifying the current model To remove selected atoms from the current model select the Edit Cut menu item or press lt Alt gt x on the keyboard These atoms can then be pasted into the same or another model space To make a copy of selected atoms from the current model select the Edit Copy menu item or press lt Alt gt c on the keyboard These atoms can then be pasted into the same or another model space To paste atoms that were previously cut or copied from the same or a different model space into the current model space select the Edit Paste menu item or press lt Alt gt v on the key board If all the atoms to be pasted correspond to atoms in the current model they are pasted to an offset position Cerius Modeling Environment April 1999 207 6 Managing Modelsand Sessions Important In addition to the selected atoms any bonds and hydrogen bonds between the selected atoms and linkages on selected atoms are copied into the paste buffer Other information such as monitors and subunit or chain information if present is not copied into the paste buffer Copying models to and from other applic ations Timeout period The cut or copy and paste operations described in the previous section make use of your computer s clipboard Thus applications that can work with information stored in the system cli aphoard can make use of these structural elements as does Cerius
37. just as they do in the Sketcher control panel Performing simple and complex selections and simple editing of your selections You can also access many of these subtopics directly by selecting the Help Topics menu items Select the Help Examples menu item The Example files control panel allows you to load and automati cally play back some pre recoreded examples of many things that can be done with Cerius Most of these examples use other mod ules in addition to the basic Visualizer controls Try some of them You must of course have licensed copies of any programs used in these tutorials Select the Help About Cerius2 menu item The About Cerius2 control panel contains information on contacting Molecular Simulations Inc It includes our website s URL and the email and other addresses for obtaining customer support 39 Experimenting with other features of the interface Now that you ve gained some familiarity with Cerius you can explore more of its features on your own You cannot cause any permanent damage Unless you specifically save for example changes you make via the Utilities Customize menu items Cerius will revert to all its default settings the next time you start it You can use the File New Session menu item to in effect restart Cerius without actually quitting and reloading it Many module cards have a Reset function which returns con trol settings to their def
38. skills you ve learned Related material points you to MSI documentation that pro vides more detailed information about the functions introduced in the tutorial exercise Cerius Modeling Environment April1999 93 3 Tutorials Before you begin To complete this tutorial you need a licensed copy of Cerius and a directory into which you can save the files you create during the tutorial In this tutorial you learn about the Cerius Graphs card Nearly all the Cerius materials science modules produce some output to the graph window It s important that you understand how the Graphs card works so that you can get the most from your graphical results You can use the functions on the Graphs card To load and save graph files To edit text on graphs To set new colors and plotting styles To make graphs and data sets visible or invisible To combine data sets from different graphs To control version over writes You have opportunity to do all these things in this tutorial exercise Cerius Graphs terminology The Cerius graph system is based on a hierarchy of three structures Gallery Graph Data set These are defined below and shown symbolically in the figure Data set At the bottom of the hierarchy is the data set The data set must be one of three types An array of xy coordinates for a normal 1D plot Aset of grid points with an intensity or a contour height for a 2D cartesian plo
39. tivity crystal cell parameters symmetry information and charges Symmetry information is written out and read in as General Posi tions MSF files are suitable for crystal and nonperiodic structures Note MSF files are not written in ASCII format you cannot edit them 418 Cerius Modeling Environment April 1999 Struc ture files Record 1 FILTYP 2 DESCRP 3 REMARK 4 FORC EFIELD Format A6 I5 The Molecular Simulations BIOGRAF BGF format allows com munication with the BIOGRAF POLYGRAF and NMRgraf pro grams BGF files default file extensions bef or xtl are suitable for periodic and nonperiodic structures storing element types coor dinates connectivity data and charges For periodic structures space group and space group table number are also stored Cerius reads in POLYGRAF monomers with H atoms labeled as Head and Tail and substitutes Cerius Head and Tail atoms When saving Cerius monomers in the BGF format POLYGRAF Heads and Tails are substituted for their Cerius equivalents Cerius crystals are written as periodic POLYGRAF BGF files On importing crystal details from these periodic files are read into the Cerius data structures although the crystal cell is not automati cally reconstructed The significant records recognized by Cerius are described in terms of FORTRAN edit descriptors in the following table Storage File Header BIOGRF or XILGRF for penodic f
40. you review sketching while also learning some important new things How to duplicate a model How to select by fragment How to move one fragment relative to another 84 Cerius Modeling Environment April 1999 Managing Modelsand More 1 Sketch the indigo model Create a new model space by choosing the button on the Model Manager Rename this new model space indigo You re going to sketch the indigo model in this space Because indigo is centro symmetric save time by sketching only half of the molecule and then doubling it H NAAN co N r Halfan indigo molecule aa H i O 2 Sketch this fragment Hint you may want to begin by using the template tool with the phenyl fragment Choose the Select All item from the Edit pulldown menu or the Ba icon All atoms are highlighted Choose the Duplicate item from the Edit pulldown menu Cerius Modeling Environment April 1999 85 3 Tutorials A second copy of the molecule is pasted into the model window Pick in the Model window and hold down the left mouse button while you drag the mouse to create a box enclosing the whole of one molecule Hold down the lt Ctrl gt key and use the rotate and translate mouse controls Only the selected molecule moves Move one fragment relative to the other until the two car bon atoms at the ends of the five membered rings are about a
41. 1999 Controls and control panels Close button CALCULATE close contacts eee h betwee atoms Action buttons in model DELETE all close contacts Contact Criteria Radio buttons Cut off id YDW Ratio 0891 Labelled action button that opens another contol l pane Display Style Check box i Annotate close contacts Popups Text Colo Line Color pups E Cerius Modeling Environment April 1999 139 4 The Cerius Interface Types of contols Color coding Labels and shape Functions of typical con trols Tip Functions of specific con trols Buttons in the control panel window border Different types of controls are distinguished by their appearance For instance popups are yellow two state controls which can be on or off checked or unchecked etc are purple or green respec tively and buttons that perform an immediate action when clicked are blue A control s function is generally indicated by labels words on or next to the control and or by a graphical icon A control s function may also be suggested by its shape e g a slider or a dial which you manipulate by clicking and dragging Except for the deck of cards itself all buttons and menu items that provide access to a control panel are followed by an ellipsis For example selecting a menu item or clicking a button labeled Preferences brings up a control panel that enables you to set related pref
42. 2D polar 302 axes 300 axis labels 299 300 axis ranges 301 cells 300 Cerius2 296 color 303 304 computer memory 307 308 309 contours 304 contracting 303 creating 294 data sets 294 295 299 defaults 306 delayed update of display 298 dette 294 E ESA displaying 298 editing 299 emphasis 270 expanding 303 files 296 297 309 428 finding coordinates 298 formats 305 gallery 297 298 hiding 298 hkl labels 300 HRTEM output 302 immediate update of display 298 Insight II 396 keys 299 300 line 294 loading 296 307 magnifying 303 managing 307 point 294 preferences 306 printing 259 radius in 2D polar 302 regenerating 307 removing 308 removing data 299 replacing 307 resetting view 302 303 retaining 307 308 saving 309 scaling 301 302 scrolling 301 302 selecting 298 selecting data 299 shading 305 shifting data sets along y axis 301 302 shrinking 303 style 299 303 304 tables as source of data 363 title 299 300 types 294 295 x y 294 x y z 295 zooming 303 GRAPHS card 292 Graphs Expert Functions control panel 306 307 308 309 Graphs module 292 grid mode tool 38 group defined 353 Groups control panel 162 GUL definition 127 H H ADJUST button 157 H Bond Calculation Preferences control panel 184 help on screen 397 Help menu 45 135 help on screen 2 28 130 135 high coordination centers 169 histograms 294 HYBRID 243 hybridization default 169 editing 169 OTHER option
43. 305 Preventing replacement of old graphs 307 Removing graphs and data from a Cerius session 308 Saving graphs 6 eee 309 11 Working with Tables 311 Introduction to Cerius tables 0 ccc eee eeee 314 The table window 0 0000 cece eee eee 314 Keeping track of the current table 316 Managing and editing tables 00 0000 eue 316 Creating a new table 0 6c cc eee 317 Loading and reloading tables 05 318 Importing an ASCII text file into a new table 319 Specifying the current table 1 0 0 0 00000 320 Entering values and editing individual cells 320 Copying Oe and clearing information 322 Inserting and deleting entire rows or columns 324 Table expansion and cursor control 326 Saving atable o enia a oe aa aa ie a ee 326 Closing a table er mapear a ana 327 Table style and display 0 0 ccc eee eee 327 Aligning information within columns 328 Assigning data typeS 2 cece eee 329 Setting display formats 06 00 cece nnn 330 Specifying headings and banners 4 331 Changing row column and heading sizes 332 Values and mathematical expressions 333 Applying mathematical expressions to cells or columns334 Entering mathematical expressions 337 Using numbers 1 06 66 eee eee 338 Cross references 00 cee eee eee eee 343 Calculations on models
44. 399 neutron scattering 187 NO LABEL 243 noncritical entry defined 271 NUMBERS 243 numbers double precision 140 O OCCUPANCY 243 occupancy saving 210 specifying 154 Off Color Selection control panel 275 On Color Selection control panel 275 on screen help 130 135 142 Open Table control panel 318 319 OpenGL mode 279 Orient View control panel 234 235 237 240 Outlier Handling control panels 277 out of plane angles measuring 221 overlay mode tool 39 P Page Setup control panel 260 261 Panel Manager control panel 392 393 394 passwords 386 pattern transparency defined 279 PDB file format 426 Pen Colors control panel 268 269 270 periodic structures 191 199 building 150 periodic table 33 tool 33 Periodic Table window 180 265 linking to control panels 166 pick targe defined 161 pick definition 132 Plane tool 220 planes angle between 220 Playback Script control panel 380 Plot Table control panel 363 364 365 Plotting Attributes control panel 300 301 302 304 305 polymers 191 popups 140 using 12 Position Atoms control panel 177 positional disorder 185 positional light defined 280 PostScript output 288 preferences 214 loading 214 startup scripts 381 Print control panel 260 261 printing 41 259 color 260 command 260 detail 260 file sizes 261 format 260 graphs resolution 261 previewing 261 quality 258 260 raster 260 resolution 261 time 261 to a printer 260 to file 260 vector 260 Proc
45. Atom Selection control panel see Additional selection criteria Not all combinations of pick target selection criterion and selec tion scope make sense or are allowed The supported combina tions are shown in Table 2 Select the Edit Selection menu item to access the Atom Selec tion control panel This control panel enables you to specify the Pick target Select atom s which are and Within criteria when the mouse is used for selection see Selecting according to properties In addition more selection criteria are available These functions are not linked to mouse activity in the model window but occur when an icon or action button in the control panel is clicked For example you can select all atoms within a specified radius of a selected atom all atoms in a named group or all backbone atoms in a polymer See also Defining and selecting groups and Customized atom selection Please see the on screen help for details on the functioning of each control in the Atom Selection control panel Defining and selecting groups Defining groups You can define any collection of atoms as a group and then per form group based selections To define and name such groups access the Groups control panel by selecting the Edit Groups menu item You can also rename redefine or delete the group definitions 162 Cerius Modeling Environment April 1999 Selecting atomsand groupsof atoms Table 2 Possible combinations o
46. Atoms control panel More than one atom should be selected You can specify the rota tion axis and center in Cartesian XYZ crystal ABC or surface UVW coordinates Alternatively you can specify that the axis be calculated as the best fit line through the currently selected atoms and or the rotation center as their geometric center You can change which atoms are currently selected for specifying each definition If symmetry constraints do not allow the requested rotation the closest permitted rotation is made instead Please see the on screen help for details on the functioning of each control in the Rotate Atoms control panel You can rotate the selected atom s by clicking and dragging a slider or a dial or by entering the angle in the associated entry box Aligning and positioning atoms Aligning atoms To accurately align selected atoms with respect to a coordinate sys tem select the Move Atoms Align menu item to access the 176 Cerius Modeling Environment April 1999 Additional information Positioning atoms Additional information Basic editing Align Atoms control panel You specify one intra model vector that is to be aligned with one coordinate axis and another intra model vector to be aligned with a coordinate plane that includes that axis You also specify the point about which the selected atoms are rotated You specify the intra model vectors to be aligned with the coordi nate axis and plane
47. Deleting applies only to entire rows or columns It removes both the information and the row or column from the current table Inserting and deleting entire rows or columns You can insert or delete entire rows or columns 324 Cerius Modeling Environment April 1999 Related information Inserting columns and rows Tip Deleting columns and rows Caution Managing and editing tables Selecting columns rows and cells is presented in Selecting rows and columns The differences between cutting clearing and deleting are summarized under Technical notes on copying cutting and past ing To insert a new empty column to the left of the selected column or current cell or to insert a new empty row above the selected row or current cell Click the INSERT tool in the current table tool bar or Select the Edit Insert menu item from the TABLES card If you selected only a cell choose Row or Column in the message window that appears Select two or three four or more rows or columns if you want two or three four or more respectively new empty rows or columns to be inserted To insert a new column on the far right side of the table or a new row at the bottom of the table please see Table expansion and cursor control To delete the selected column s or row s or the column or row containing the current cell Click the DELETE tool in the current table tool bar or Select the Edit Delete
48. Edit box of the User Graph is toggled on and that the Display boxes for the Emix Fit and the Thermo dynamics graph are toggled off Open the Graph Manager control panel by clicking the Graph Manager button on the Gallery Manager control panel Toggle on the Display boxes for the Enthalpy and the Free Energy data sets Cerius Modeling Environment April 1999 111 3 Tutorials These two datasets are plotted on the User Graph Vatitled Optional You may want to review what you learned in the previous exercises pages 100 106 by customizing this graph altering plot style changing colors scaling axes and editing text 2 Delete extra graphs from the Gallery Open the Graphs Expert Functions control panel by choos ing Gallery gt Expert Functions from the Graphs card In the Graph Chooser list box of the Gallery Manager con trol panel choose to display only the Emix Fit graph Click the CLEAR button on the Gallery Manager Graphs Expert Functions control panel Clicking the CLEAR button deletes from the Gallery Manager all graphs that are not currently on display in the graph window The Graph Chooser list box should now look like the figure below the Thermodynamics and the User Graphs graphs are gone 112 Cerius Modeling Environment April 1999 Managing and Modifying Graphs 3 Adda second graph Set the Data Placement popup of the Graphs Expert Func tions control pa
49. Editing element and bond attributes Control of the tionality Saving a constructed model Saving preferences Basic building model cleaning function Saving model structure files Using saved sessions as preferences settings Why read this section This section tells you where to access the basic building tools and how to perform tasks that are typically associated with building the basic skeleton of a small model It contains information on Starting to construct a new model 146 Cerius Modeling Environment April 1999 Related information You should already know Basic building Adding atoms and bonds Adding templates groups of atoms Fusing and connecting fragments Adding hydrogens Basic editing tasks including changing element types bonding and model conformation are presented under Basic editing The final task you would perform for building almost any model would be to optimize its configuration Refining the conformation Storing models in files is presented under Saving model structure files Selecting atoms is presented under Selecting atoms and groups of atoms Tasks that may be less often or less typically performed such as editing atom attributes and changing defaults and preferences are covered in Advanced building and editing If you have never used Cerius before or are unfamiliar with the terminology used to indicate how to use its interface please go through the model building example
50. Environment April 1999 Values and mathematical expressions Table 12 Unary math operators in Cerius table expressions Operator Retums Description neg number Negation rand number Random number between zero and x sign number Retum 1 if x gt 0 0 retum 0 if x 0 retum 1 if x lt O spline number Retum x if x gt 0 0 otherwise retum zero sqrt number Square root Binary math operators Binary mathematical operators Table 13 are placed between two values both of which must be or evaluate to numbers Mathematical operations using binary mathematical operators are evaluated using algebraic logic in the standard order of prece dence You can use parentheses to alter the order of precedence Examples of expressions including binary mathematical operators are L2 eS 4 col 6 7 col Concentration 2 7 col Concentration 2 The column references see To columns in this example all eval uate to numbers If division by zero is attempted an error message shows the row and column where the error occurred and the cell is set to null Table 13 Binary math operators in Cerius table expressions Operator Description Addition Subtraction Cerius Modeling Environment April 1999 339 11 Working with Tables Table 13 Binary math operators in Cerius table expressions Operator Description x Multiplic ation Division Modulus mod Modulus Exponentiation Statistical opera
51. If your session contains several models you should know how to specify the current model Specifying the current model You may also want to know how to select atoms in several models Selecting atoms in several models Moving models on the screen Changing the position viewing angle and magnification of mod els in the model window aid in tasks such as accessing parts of the model viewing small parts of the model in detail understanding 230 Cerius Modeling Environment April 1999 Finding information Related information Moving models on the screen the model s 3D structure bringing related or complementary models together in space optimizing displays for printout This section includes information on Basic tasks and methods Moving models relative to one another Superimposing models Storing and retrieving views Moving parts of models is discussed under Editing the structure Copying models or parts of models from one model space to another is discussed under Moving models between model spaces Basic tasks and methods Finding information Display axes Note Basic model viewing tasks can often be accomplished in several ways by using the mouse in the model window using tools in the toolbar of the Cerius e Visualizer s main control panel using con trol panels accessed from menu items in the main control panel mainly from the View menu or using keyboard shortcuts The various methods differ in c
52. Isosurface imports only grd and mbk format files so data from non Cerius applications must be converted to these formats It is most convenient to convert to ASCII grd format when necessaty While most applications in Cerius have customized panels for grid manipulations Isosurfaces offers a wider range of options It makes it convenient to manipulate a large number of surfaces it allows stepwise progress through a range of isocontour values and it lets you use grid files created with external applications The basics of starting Cerius and using its interface are demon strated in Introducing Cerius2 and described in The Cerius2 Inter face Grids in Cerius are produced as output from calculations in vari ous other application modules How to set up and run the appro priate calculations are discussed in the documentation for the relevant application modules The tools for handling isosurfaces are accessed from one of the decks of cards in the main Visualizer control panel To access the TABLES amp GRAPHS module click the deck selector and choose TABLES amp GRAPHS from the list that appears Then click the title of the ISOSURFACES card to bring it to the front The deck of cards menu area should now look like this Cerius Modeling Environment April 1999 369 12 Working with Isosurfaces Ea _rasLes a crapns m Analyzing 3D grid properties Three dimensional grid properties such as orbitals densities
53. It describes the integrated set of tools for session management and atomistic modeling that form the core of the Cerius modeling environment Topics described include molecular modeling tasks and their asso ciated Cerius procedures combining conceptual procedural and reference material in one comprehensive information source You need not read this entire documentation set before you start using Cerius First time users should read Introducing Cerius2 first Everyone should read How To Use This Guide which introduces the Cerius modeling environment and at least skim these sec tions which describe how to perform basic modeling tasks The Cerius2 Interface Building Models Managing Models and Sessions Geometry Analysis Viewing and Displaying Models You can glance through the headings in these sections which describe modeling and other tasks that typically are performed less often or by fewer users Enhancing Model Display Working with Graphs Working with Tables Cerius Modeling Environment April1999 1 1 How To Use This Guide Scripts and Licensing Customizing the Interface You can then read those sections that describe the tasks you want to perform and or tools you want to use Reference material is contained in these sections References Definitions Mouse and Keyboard Actions File Formats Who should use this guide Prerequisites This documentation set is intended mainly for day to day
54. Label atoms by element type Open close and move control panels Display help text panels for control panels and menu items Re initialize and exit from Cerius Cerius Modeling Environment April1999 61 3 Tutorials You may now want to proceed to the next tutorial Using the 3D Sketcher where you learn how to build your own models Alternatively you may want to learn more about the Visualizer by reading the user manual sections listed below Related maternal The Visualizer is discussed in detail in the Cerius Modeling Environ ment The sections listed here will provide you with more detailed information about atom display and selection than are included in this tutorial book 1 Sections in the Introducing Cerius and Viewing and Displaying Models chapters of the Cerius Modeling Environment 2 The section Selecting atoms and groups of atoms in the Building Models chapter of the Cerius Modeling Environment 3 The Managing Models and Sessions chapter of the Cerius Modeling Environment Using the 3D Sketcher This chapter contains a tutorial on molecular sketching It intro duces the Cerius 3D Sketcher You learn how to draw and edit mod els in 3D and how to use the Clean function to do simple optimization of model geometry You also learn how to save the models which you build into structure files This chapter is divided into three parts Before you begin provides some introductory and ba
55. Molecules module which is separately licensed and documented and is typically found in the DRUG DIS COVERY deck of cards offers additional functionality for compar ison of model structures Storing and retrieving views Storing a view Retrieving a view Additional information You can save the current view that is the model and its viewing conditions such as orientation location magnification in memory for later retrieval during the current session Up to ten views can be saved and retrieved for later viewing within the current session To store a view select the View Orient menu item to access the Orient View control panel Set the View A J popup as desired and click the STORE pushbutton To retrieve a view select the View Orient menu item to access the Orient View control panel Choose the desired view from the View A J popup and click the RETRIEVE pushbutton Please see the on screen help for details on the functioning of each control in the Orient View control panel 240 Cerius Modeling Environment April 1999 Animating models Animating models The Visualizer animation facilities enable you to create an anima tion sequence from a trajectory file such as that produced by the Cerius Dynamics Simulation module and then replay that sequence using VCR style controls You should already How to produce trajectory files is discussed in the documentation know for the relevant application modul
56. POL_diff_am log Alternatively you may want to learn more about the graphs in Cerius by reading the user manual selection listed under the Related material heading below You may now want to proceed to the tutorials in Cerius Materials Sciences Tutorials or Cerius Life Sciences Tutorials or you may prefer to explore other Cerius modules on your own with the aid of the Cerius user s reference books and the on line help text Related material 1 The Graphs chapter of Cerius Modeling Environment 2 The File Formats appendix of Cerius Modeling Environment Basic Molec ular Simulation Minimization amp Dynamics This chapter shows how to use molecular mechanics techniques to simulate the behavior of a system on an atomistic scale The example used is a simulation of beta D glucose in water The tutorial has four parts A Building an initial model of the glucose molecule using the 3D Sketcher Cerius Modeling Environment April 1999 117 3 Tutorials C D Refining the model using molecular mechanics minimization to optimize bond lengths angles etc Adding water for the purposes of this tutorial only a small amount of water is included Simulating the behavior of the glucose water system over time using molecular dynamics The purpose of this lesson is to introduce the most basic tools for atomistic level simulation More advanced simulation and analysis options are described in Cerius T
57. R5K and above processors If some of the color controls do not work you could try issuing this command gt setenv FORCEOPENGL 1 before starting Cerius Please see the Installation and Administration Guide for additional information If you prefer to learn by doing you can skip the following discus sion of concepts and proceed to Accessing the tools This section includes information on Adjusting global light settings Defining discrete light sources Setting the graphical quality and screen resolution is discussed under Resolution and graphical quality The screen coordinate axes are shown in Figure 3 Cerius Modeling Environment April 1999 279 9 Enhancing Model Display Concepts An understanding of the following concepts can help you use the lighting controls effectively The global ambient light as controlled directly on the Lighting control panel is general lighting in the scene that does not appear to come from any particular source The ambient light component of defined lights is light that is scat tered so much by reflection from the walls enclosing the vir tual scene and from objects within the scene that there is no way to determine its original direction Ambient light tends to take on the primary color of the surroundings and is most apparent in parts of the object that do not receive direct illumi nation Diffuse light is scattered from an object in all directions specular light appea
58. Save Table control panel Click the SAVE AS tool in the table manager tool bar or Select the File Save As menu item from the TABLES card Enter a filename in the entry box and click the SAVE pushbutton to save your file Use of the file selection list box and other file selector controls to navigate the directory structure is presented in detail under Find ing model file s Creating your own directories or subdirectories is described in Making custom directories A file that has been saved previously can be saved again without using the Save Table control panel To resave a file in the same directory and with the same filename as before 326 Cerius Modeling Environment April 1999 Saving only part of a table Additional information File formats Table style and display Click the SAVE tool in the table manager tool bar or Select the File Save menu item from the TABLES card If the current table has previously been saved to a file it is resaved as the same file overwriting the previous version If the file has never been saved before the Save Table control panel Saving and naming a table file appears so that you can name the file and specify a directory in which to place it If you want to save only part of a table in MSI format you need to export the table Exporting table information Please see the on screen help for details on the functioning of each control in the Save Table contro
59. Selection mode icon once more Change the Edit Bond popup from Single to Double and click any carbon atom Pick an adjoining carbon atom 70 Cerus Modeling Environment April 1999 Using the 3D Sketcher A dotted guideline appears and then becomes the double bond between the carbon atoms Repeat to make alternate bonds in the ring double 3 Adjust the hydrogens and minimize the model Use the H Adjust and Clean buttons then rotate and view this planar benzene D Editing benzene to make phenol In the following steps you add an OH group to benzene to make phenol Also you learn how to use the Sketcher tools to alter torsion angles bond angles and bond lengths 1 Add an oxygen Use the popup adjacent to the Edit Element text box to select O for oxygen Cerius Modeling Environment April1999 71 3 Tutorials The popup is a fast way to choose commonly used element symbols Select the periodic table icon after this popup A periodic table appears Select any element in the table The element is written to the text box You can also change the element by typing a new element symbol into the Periodic Table text box Close the periodic table If necessary restore the Edit Ele ment symbol to O Pick any one of the hydrogens to change it to an oxygen In Edit Element mode the mouse cursor is a circle Use t
60. This enables you to cut and paste structural elements back ue forth between Cerius and other ape icuors such as Insight II ISIS Draw ChemDraw Catalyst and Open Inventor based applications on SGI systems that have the Molecular Inventor Exe cution Only Environment molinv_eoe installed However other applications may not be able to use all the information associated with Cerius structural elements Transferring large models between Cerius and other applications can take up to a minute or more Cerius is configured to wait up to 3 min for information pasted from other applications to com plete transfer Howey transferring large models or structural elements from Cerius to other applications may fail if the other application s timeout value is not increased The default timeout period for most applications paste operations is 5 30 s depending on the operating system If you have problems pasting large mod els from Cerius to other compatible programs you can usually increase the other application s timeout value by adding an entry to the Xdefaults file in your home directory For example to increase the timeout value for SGI s InPerson application add the following entry InPerson selectionTimeout 180000 This changes the default selection pout value to 180000 ms 3 min The default value for Cerius is 180000 but you can also change it in your Xdefaults file using this format Cerius2 selectionTImeout
61. a file Additional information File formats Saving graphs produced by Cerius modules enables you to keep a record of your results Saved graphs can be loaded back into a Cerius session Loading graphs for printing or for comparison with other graphs A saved graph file contains all graphs and data sets just as they appear in the current graph window Unless a graph and its desired data set s are actually displayed in the graph window the graph is not saved even if it is currently in computer memory Creating your own directories or subdirectories is described under Making custom directories To save graphs from the current Cerius session select the File Save Graphs menu item from the GRAPHS card to access the Save Graphs control panel Once you have located the directory in which you want to store your graph click the SAVE pushbutton Use of the file selection list box and other file selector controls to navigate the directory structure is presented in detail under Finding model file s Please see the on screen help for details on the functioning of each control in the Save Graphs control panel Cerius saves graphs in grf format and automatically adds grf to the filename if you have not specified some other extension Cerius Modeling Environment April 1999 309 10 Working with Graphs 310 Cerius Modeling Environment April 1999 n Working with Tables In Cerius you can create your own
62. acquainted with the interface optional Please feel free to take some time to explore the Cerius interface on your own You can t break anything Cerius Modeling Environment April1999 7 2 Introducing C erius Try using the left and right mouse buttons to click various buttons and other controls If a list of items appears continue to hold the left mouse button down and release it over an item to choose that item Try building or loading a model if you want Important P If you do anything in this optional step you should clean up the interface so that you can make a fresh start when you begin building your first model as follows Use the mouse to move the cursor over the File menu at the top left corner of the main control panel Click with the left mouse button and drag the cursor down to New Session Release the mouse but ton When a small window labelled Re initialize All appears click its Confirm button with the left mouse button Everything now goes back to its condition when Cerius first loaded If you moved any main windows you should put them back to where they were when you started You can close any open control panel by left mouse clicking in the box JH in its upper right corner Building a model caffeine 4 Locating the basic building tool The top of the Visualizer main panel contains a menu bar a row of menus that looks like this Use the mouse to move the cursor over
63. adjust their relative number To do so select the View Display Attributes menu item to access the Display Attributes control panel Click the Pref erences pushbutton to access the Style Preferences control panel Adjust the Resolution sliders by dragging or directly enter values in the associated entry boxes for Spheres Cylinders and or Ellipsoids To change the line width used to draw non cylinder bonds select the View Display Attributes menu item to access the Display Attributes control panel Click the Preferences pushbutton to access the Style Preferences control panel Adjust the Line Width slider by dragging or directly enter values in the associated entry box Cerius enables you to specify the quality of graphics displayed on the computer and written to vector PostScript files Three quality settings are available standard better and excellent Higher qual 258 Cerius Modeling Environment April 1999 Additional information Printing models and graphs ity settings reduce the golf ball effect that results because X and vector PostScript triangles are flat shaded instead of color interpo lated However each higher quality setting can also increase both the file size and the rendering time by a factor of four over the pre vious quality setting This quality setting is independent of the resolution settings for spheres cylinders and ellipsoids Object resolution This setting applies to the number of s
64. and the rotation center using Cartesian XYZ crystal ABC or surface UVW coordinates Alternatively you can specify that the first intra model vector the one to be aligned with a coordinate axis be calculated as the best fit vector through the currently selected atoms Similarly you can specify that the second intra model vector the one to be aligned with a coordinate plane be calculated as the best fit vector through the currently selected atoms You can also specify that the rotation center be cal culated as the geometric center of the currently selected atoms You can change which atoms are currently selected for specifying each definition If symmetry constraints do not allow the requested alignment it is not performed Please see the on screen help for details on the functioning of each control in the Translate Atoms control panel To accurately position selected atoms in space select the Move Atoms Position menu item to access the Position Atoms control panel You specify both a reference point and a destination point then the selected atoms are moved in a way that maintains their spatial relationship with the reference point i e the reference point is moved together with the atoms You can specify the reference and destination points in Cartesian XYZ crystal ABC or surface UVW coordinates and or spec ify that these points be calculated as the geometric center of the currently selected atoms You ca
65. as dotted lines indicating what planes were used Torsions Measuring torsions To measure the torsion angle involving any four atoms you use the Torsion tool You can use it in two different ways 220 Cerius Modeling Environment April 1999 Related information Measuring models Select the Torsion tool and then pick sets of four atoms whose dihedral angles you want to measure These atoms need not be bonded to each other The angle s in degrees are indicated in the model window or Select any number of atoms and then double click the Torsion tool The angles in degrees of each existing torsion among four consecutively bonded selected atoms are indicated in the model window Dotted lines indicate what torsion was measured Information on examining and changing torsions is contained in Examining and changing torsions Inversions Measuring inversions or out of plane angles To measure the inversion or out of plane angle involving any four atoms you use the Inversion tool These atoms need not be bonded to each other The vertex atom is the first one picked First set the definition according to which the inversion is calcu lated with the Inversion popup Then you can Select the Inversion tool and then pick four atoms whose inver sion out of plane angle you want to measure or Select the desired four atoms and then double click the Inver sion tool These atoms need not be bonded to
66. bond length apart Link the two fragments by a double bond using the Edit Bond option in the Sketcher Clean to complete the indigo molecule Return the Sketcher to selection mode and then close the Sketcher control panel D Measuring the indigo model tong 4 H R c H Il es II ar No ye7 Ny il ee H ae H In the following steps the Measurements control panel is used to measure the geometry of the indigo model from C Building a model of indigo 86 Cerius Modeling Environment April 1999 Managing Modelsand More 1 Measure the distance between two atoms Open the Measurements control panel from the Geometry pulldown menu Click on the Distance icon As in the Sketcher these icons determine the function of the mouse in the model window Pick any two atoms The distance between them will be marked on the model You may need to rotate the model or zoom in on it to see the measurement clearly 2 Try some of the other measurement tools Pick three atoms to measure angles four to measure tor sions or inversions and six to measure the angle between two planes Choose the List Measurements button Pick three atoms to measure angles four to measure torsions or inver sions and six to measure the angle between two planes All measurements you have made will be written out to the text win dow You may want to label the model by Numbers to m
67. build up a composite model The for merly separate models are now considered one model The simplest way to copy a whole model to a new model space is to make sure the desired modelis current then select in order the 206 Cerius Modeling Environment April 1999 Example Handling multiple models Edit Copy and Edit Paste menu items A new model space is cre ated automatically If you have the display in border mode How they are displayed anyway make sure the correct model is current Specifying the cur rent model Then simply click in empty space within a border pane whose contents you want to copy and drag the cursor into the cur rent model space s display pane lower left of the model manager Clicking an atom in a border pane selects that atom Selecting atoms in several models You can also select all atoms in a model and use cut or copy and paste Moving parts of models from one model space to another to move entire sets of atoms from one space to another Nonatomic infor mation if any is not copied by this method A tutorial example of copying model space contents from one space to another can be found under Copying models from one model space to another Moving parts of models from one model space to another You can also copy or move parts of models from one model space to another or within the same model space using atom selection Selecting atoms and groups of atoms and editing techniques for
68. can all be used to store isotropic and anisotropic temperature fac tors Temperature factors The DBWS file format can be saved and read only by using the Rietveld DBWS menu card not by using the Visualizer The conversions made between the stored file format and the Cerius format use the assumptions described below MSI The MSI structure file format Uses Uiso and U j formats Order is Uy U22 U33 U12 U23 U13 SHELX The SHELX Siemens 1990 structure file format Uses Uiso and U j formats Order is U11 U22 U33 U23 U13 U12 Cerus Modeling Environment Apnl 1999 427 D File Formats ICSD DBWS MolEN The ICSD Fachinformationszentrum 1991 structure file format Uses U Uses Ui Bij and Bij Order is Uy Un U33 Ur U13 U23 and Biso B cross terms include a factor of two in the term The DBWS 1991 structure file format Uses Biso and Bij Order is B11 B22 B33 B12 Biz Bas B cross terms do not include a factor of two The MolEN Enraf Nonius 1990 structure file format Uses Biso and Bi Order is B11 Boo B33 Biz Bis Bas B cross terms include a factor of two in the term Files for graphical data in Cerius should be stored in files with the extension grf Cerius grf files can describe any state of the GRAPHS data structure Some example files are stored in the Cerius2 Resources EXAMPLES data directory The file format consists of a header record follo
69. choose the desired group from the Group pulldown Enter your expression in the Enter Cell Der ivation entry box using one or more of the operators described under Entering mathematical expressions Do not begin the expression with an equals sign Click the APPLY TO pushbut ton To apply an expression only once to a cell or column s so that the results are calculated and displayed but the expression is not retained use the Table Properties control panel as above except check the Apply Derivation Only Once check box 336 Cerius Modeling Environment April 1999 Values and mathematical expressions Important Applying an expression only once can save time later since these expressions are not recalculated when the table is recalculated Recalculating table values However you should not refer to other parts of the table Cross references in these expressions since these unretained expressions cannot be recalculated if you change values in any of the columns cells etc that are referred to Deleting expressions To remove an expression from the current cell or a selected column without deleting the calculated value enter an expression con taining only two quotes that is or in the cell edit win dow Additional information Please see the on screen help for details on the functioning of each control in the Table Properties control panel Entering mathematical expressions Finding information This sect
70. choosing Exit from the xps view File menu in the top left corner Select one of two methods to print the file There are two ways that you can print the file The first is to change the PostScript Destination back to Printer and choose the Print button If the laser printer that you want is not the system default you will also need to edit the print command Ip c Or The second is to print the trinitrophenol ps file from a UNIX shell in the way you would normally print any PostScript file In the simplest configuration the print command would be Ip trinitrophenol ps Cerius Modeling Environment April1999 91 3 Tutorials On the Page Setup control panel set the background Color popup back to Black The model window background returns to black You may have found that the white background is hard on your eyes It is also possible to use the SGI snapshot utility or the xv program to capture rgb images from Cerius 5 Exit or continue to another tutorial Either Re initialize the program by selecting New Session from the File pulldown menu and choosing the Confirm button on the Re initialize dialog box Re initialization resets all the Cerius control panels to their original defaults Alternatively if you want to stop now Choose Exit from the File pulldown menu to quit from Cerius and choose the Exit button on the Exit Option dialog box
71. color is always the same as the outline color To set or change the line width of an annotation object except for text enter a number in the Line Width entry box To set or change the properties of text annotation objects Use the entry box to the right of the Text tool to specify the text content Set the font and style pulldowns as desired These are located below the Text tool Set the size by entering a font size in the size entry box or choos ing a value from the associated popup You can move change the size of delete or hide annotation objects To move an object click the Move tool Click an object with the left mouse button and drag in the model window to move it To change the size of an object click the Resize tool Click the end corner or edge of an object with the left mouse button and drag in the model window to resize it You can also change the shape of rectangles and the orientation of lines and arrows with this tool To delete an object click the Delete tool Click the desired object s with the left mouse button to delete them To hide all annotation objects check the Hide All check box To display them again uncheck the Hide All check box Cerius Modeling Environment April 1999 247 8 Viewing and Displaying Models To delete all annotation objects click the Delete All action but ton Recovering from mistakes An UNDO pushbutton provided at the top of the control panel
72. colors select the View Colors menu item to access the Color Selected Objects control panel Set the Pen popup to DEFAULT Tip You can also access the Color Selected Objects control panel by selecting the Build Annotations menu item to access the Annotation control panel then clicking the More Colors pushbutton 266 Cerius Modeling Environment April 1999 Additional information Model display colors Please see the on screen help for details on the functioning of each control in the Color Selected Objects control panel Coloring atoms by properties Accessing the tools Coloring atoms accora ing to a property Coloring a model accora ing to multiple maps Returning to default atom coloring scheme Cerius enables you to color atoms according to properties such as charge whether atoms are fixed or moveable mass radius etc as another aid to abstracting information from your model Select the View Colors menu item on the main Visualizer con trol panel to access the Color Selected Objects control panel This control panel can also be accessed by selecting the Build Annota tion menu item and then clicking the More Colors pushbut ton in the Annotation control panel To color atoms according to a property simply select them and choose the desired property from the Color by a Property list in the Color Selected Objects control panel You can create your own color maps for additional
73. control panel On the Page Setup control panel set the background Color popup to White The model window background turns to white A white background will save toner when the image is printed If you want your name or any other text to appear on the image type into the User Name and Title Text boxes Cerius Modeling Environment April1999 89 3 Tutorials Scale Factor Legends Include Cerius2 Logo User Name Title Text tutorial example Grayscale Model Window Set Background Color WHITE Brightness 1 00 Create Vector PostScript Make sure that no windows or control panels are overlap ping the Model Window Choose File to be the PostScript Destination and enter trin itrophenol ps in the text box that currently reads CERIUS ps Choose the Print button A message is written to the text window Starting to output image SS E E tid ave aineceven gts Image Captured 90 Cerius Modeling Environment April 1999 Managing Modelsand More The PostScript image will be written to a file called rinitrophenol ps If you are running Cerius on an SGI choose the Preview button If you are running on another platform skip to step 4 below This calls the xpsview program to give a preview of how the PostScript image will look on the page The preview gives you a chance to alter the model view or the page setup controls before printing Close the xpsview window by
74. control panel to load a few 2 4 more models If you want a model from a different subdirectory you can double click to go up one directory level or use the popup above the files list box to go directly to any parent directory Cerius Modeling Environment April1999 35 2 Introducing C erius Managing multiple models 29 Finding the name of the model shown in the model window Notice the column of diamonds in the model table That is these items The diamond that is highlighted in red and looks 3 dimen sional indicates the name of the current model Definition In the above example glycine is the active model It is both current activities done in control panels or with the mouse affect it and the only model visible in the model window 30 Viewing a hidden model 36 Cerius Modeling Environment April 1999 Managing multiple models Say you d rather look at ferrocene than the currently active model Click the empty diamond next to the ferrocene model name That diamond becomes highlighted and ferrocene replaces the other model in the model window You may make other individual models current by clicking their diamonds 31 Viewing several different models simultaneously Notice the column of squares in the model table That is these items n 1 2 ferroce 3 Berlinite 4 m xylene 5 glycine _imjmjmjm The square that is
75. create a new model space and to copy atoms from one model space and paste them into another You copy the phenol model into the new model space and then use the Sketcher to modify the phenol model to form picric acid 2 4 6 trinitrophenol 1 Copy the phenol model Set the current model to be phenol Select all the atoms in the phenol model You can do this with the Select All item from the ccpulldown or use the Se icon All the atoms in the current model will be highlighted Choose the Copy option from the Edit pulldown This copies the phenol model into the buffer Choose the icon on the Model Manager A new model space called Model6 is created Choose Paste from the Edit menu The phenol model is copied into the new model space Cerius Modeling Environment April1999 83 3 Tutorials 2 Edit the model to create 2 4 6 trinitrophenol Open the Sketcher and click the Fragments button Load the nitro template the templates organic nitro file Use the nitro template to create 2 4 6 trinitrophenol This molecule 2 4 6 trinitrophenol is also called picric acid Return the highlight to the selection mode icon K once more Clean the model and give it the name ferrocene in the Model Manager list OH NO2 C Building a model of indigo In the following steps you use the Sketcher to build a model of indigo In doing this
76. each other The out of plane angle in degrees is indicated in the model win dow as well as dotted lines indicating what angle was measured Cerius Modeling Environment April1999 221 7 Geometry Analysis Calculating close contacts Accessing the tools Contact criteria Exclusions Displaying too close contacts that may occur between atoms can be valuable for examining models resulting from simulations pre paring accurate models or studying model model interactions Access the Close Contacts control panel by selecting the Geome try Close Contacts menu item in the main control panel s menu bar You use this control panel to calculate and display close con tacts between all or selected atoms in one or more models Two criteria are available for determining whether atoms are too close together Ifthe distance between the atomic centers is less than a speci fied cutoff distance Choose DISTANCE and enter the Cut off in angstroms Ifthe distance between the atom centers is less than 1 r2 where is a specified ratio and r4 and r are the van der Waals radii of the two atoms Choose VDW RADIUS and enter the VDW Ratio a A 1 means that close contacts are indicated whenever van der Waals spheres are just touching each other You may want to exclude certain atom pairs from the close contact calculation You can exclude BONDED atoms or atoms in the same GROUP FRAGMENT or MODEL When excluding bonded
77. end of the bond When you use the 3D Sketcher you manually place atoms in the model window then refine the atom positions later see Refining the conformation Another builder tool the Add Atom control panel enables you to add atoms to the current model one at a time at specified coordinate positions You can use it to build models and to add to existing models Although less convenient to use than the Sketcher control panel the Add Atom control panel allows precise control over the positions of atoms which is partic ularly useful for duplicating published crystal structures or inor ganic structures To access the Add Atom control panel select the Build Add Atom menu item from the main control panel Set the element type by entering the desired element name in the Element entry box or by accessing the Periodic Table window from the Add Atom control panel Specify the coordinate system to be used for positioning atoms by choosing from a popup Cartesian coordinates XYZ crystal frac tional coordinates ABC or surface fractional coordinates UVd Cerius Modeling Environment April 1999 153 5 Building Models Other properties Placing the atom for nonperiodic 3D periodic or 2D periodic systems Then click the associated entry box and enter the exact coordinates at which to place the atom Several other atom properties can optionally be specified before placing an atom in the model window hybridization charge
78. from the main control panel see for example Managing Models and Sessions and Viewing and Displaying Models The mouse function keys and cursor keys can also be used to effect rotations translations and scaling The mouse is also used to select atoms for various operations Summaries of mouse and keyboard shortcuts available in the model window are accessible from the Help pulldown menu on the main control panel menu bar by selecting Help Topics Mouse Operations or Help Topics Keyboard Operations Informa tion on mouse and keyboard operations can also be found in Mouse and Keyboard Actions Text window Caution Cerius uses the text window primarily to display text messages However you can use it to enter shell commands prefixed by an exclamation point Tcl scripting language commands and com ments To learn more about Cerius scripting see Using Cerius Command Scripts However do not try to start programs that take over the window such as vi or rn in this window 130 Cerius Modeling Environment April 1999 Using the mouse the basics Using the mouse the basics Mouse buttons Note Cerius controls are operated with the mouse The mouse has three buttons that perform different general functions Left button the action button Used to click a control panel button drag a slider select an option from a pulldown menu or popup and so on Middle button Used by your sys
79. highlighted in cyan and looks somewhat 3 dimensional indicates the visible model Click one of the empty squares The model window becomes divided into one large square display area Cerius Modeling Environment April 1999 37 2 Introducing C erius and a border of smaller square display areas The current model fer rocene if you performed only the boxed instruction in Step 30 is in the largest square display area The model you just specified is dis played in one of the smaller square display areas Click one or more additional empty squares in the model table Each model is displayed in one of the smaller square display areas Click a square that s already highlighted in blue That model now becomes hidden Notice the display mode tools That is these tools The border mode tool is currently active Select the grid mode tool directly above the currently selected border mode tool The display is divided into 4 or 9 or 16 etc depending on how many visible models you have equal sized display areas The current model 38 Cerius Modeling Environment April 1999 Managing multiple models is displayed in the lower left corner of the model window Select the overlay mode tool the topmost one of these three tools All visible models appear in the same display area Click the border mode tool again so that the current model appears
80. if the default settings in the Isosurfaces control panel are satisfactory you can click the Cre ate New Surface action button on the Isosurfaces control panel to create and display that surface on your model Make sure that none of the surfaces in the list box is selected if you want to create and display a new surface in addition to those already displayed You can edit surfaces in several ways Change the value in the Isosurface Value Range entry box to change which iso value points within the grid are displayed when the Create New Surface action button is clicked again Check or uncheck the Show Surface check box to display selected surface s or not Click the Delete Surface action button to delete selected sur face s from the display and the Edit Surface list Change the transparency and color of surfaces with the rele vant controls at the bottom of the Isosurfaces control panel Please see the on screen help for details on the functioning of each control Mapping a property onto a surface How maps on surfaces function An isosurface connects points in space that have the same value of some parameter However you can add an additional dimension to a surface by making a property map which displays the values of another property as different colors on an existing displayed surface Cerius Modeling Environment April 1999 371 12 Working with Isosurfaces Finding your property files Map specificat
81. in Introducing Cerius2 before continuing with this section How to start Cerius the names of parts of its interface as well as basic mouse usage and how to access on screen help are covered in The Cerius2 Interface Starting to consttucta new model Strategy Why develop a strategy You can probably construct a model of almost any small model you want simply by straightforward trial and error use of the 3D Sketcher This procedure will probably be good enough if you have to build only a few models However Cerius building tools typically offer several ways of accomplishing the same end Therefore depending on the types and number of similar models you need to work with a more considered approach including the use of model building or generating tools other than those con tained within the Visualizer and not documented here may prove Cerus Modeling Environment April 1999 147 5 Building Models Task oriented information Some possible approaches Note more efficient So it should be helpful for you to obtain some familiarity with all the relevant tools as you develop your own model building style using whatever combination of tools and order of tasks that works best for your purposes This section presents information in a task oriented way generally presenting simpler or default methods first The organization assumes you would build the complete skeleton of a structure first and then edit it as desired Ho
82. in the model and graph display windows 394 Cerius Modeling Environment April 1999 Accessing the tools Examining the color coa ing system Changing the interface colors Saving the interface col ors How it works Additional information Interface look and feel Select the Utilities Customize GUI Colors menu item in the main Visualizer control panel to access the Customize GUI Colors control panel The color codes listed in the Functional color groups list box each affect a certain type of item in the interface To examine what items any color code affects click its name in the Functional color groups list box in the Customize GUI Colors control panel and hold down the left mouse button over the Show Scope action but ton All items affected by that color code are highlighted for as long as you hold down the mouse button To color related groups of interface items according to your own color scheme select the name of the color code you want to change from the Functional color groups list box Then use the red green and blue sliders or the entry boxes below them to set the propor tions of red green and blue in the final color You can reset all or selected color codes to default values by using the appropriate Reset action buttons in the control panel Color changes take place immediately and remain in force for the duration of the current Cerius session To save your customized color coding of the graphi
83. lowercase letters and can return to the native format Model data can be displayed as small 2D structure diagrams or as the chemical formula chemical name or the internal Cerius iden tification number for that model Please see the on screen help for details on the functioning of each control in the Table Properties control panel Specifying headings and banners Accessing the tools Entering and displaying row headings You can enter text into the row and column headings and choose to display the headings or the row or column numbers or both headings and numbers You can also prevent a row or column from scrolling when you scroll the rest of the table making it in effect an additional heading or banner row or column To label selected rows or columns that is enter some text to be dis played in the row or column headings or to lock the scroll func tion for selected rows or columns access the Table Properties control panel as above see Accessing the tools and set the Proper ties popup to Row or Column respectively The resulting control panel is referred to as the Row or Column pane of the Table Prop erties control panel To specify whether to show row or column headings access the Table Properties control panel as above see Accessing the tools and set the Properties popup to Heading The resulting control panel is referred to as the Heading pane of the Table Properties control panel In the Row pane
84. manager and or Hide all models except the current model or any selected models except the current model by clicking the set to invisi ble button The current model is always implicitly visible and its colored visibility indicator looks flat by default To make it remain explic itly visible even after some other model is made current click its visibility indicator so that it appears pyramidal The overlay mode grid mode and border mode display tools con trol how the model spaces are displayed in the model window Border mode To divide the model window into one large pane located in the lower left corner and which displays the current model surrounded by a border of 5 smaller panes select the border mode tool If only the current model is visible it fills the entire model window Grid mode To divide the model window into 4 9 16 or 81 equal sized panes with the current model in the lower left pane select the grid mode tool As many panes appear as are required to contain the visible models If only the current model is visible it fills the entire model window Overlay mode To display all visible models together in the same large model window select the overlay mode tool Although they are displayed together on the computer screen the models still occupy separate model spaces A tutorial example of handling multiple models is found under Managing multiple models The following picture
85. menu item from the TABLES card If you selected only a cell choose Row or Column in the message window that appears Cerius does not ask you to confirm a row or column deletion The information contained in these columns or rows is lost when they are deleted unless you previously saved the table to a file Cerius Modeling Environment April 1999 325 11 Working with Tables Table expansion and cursor contol Enabling table expansion Enabling cursor wrap Tables opened from a file and certain tables generated by Cerius modules have an initially fixed number of rows and columns You may want to allow the current table to automatically expand when you use the arrow lt Tab gt or lt Enter gt keys To enable the current table to automatically expand beyond its fixed size when you use the arrow lt Tab gt or lt Enter gt keys check the Expand Table check box in the table window To enable the cursor to wrap to the next column or row when you get to the end of a preceding column or row by using the arrow lt Tab gt or lt Enter gt keys uncheck the Expand Table check box in the table window Saving a table saving and naming a table file Resaving a table file To save a table file for the first time when you need to give it a name and specify a directory in which to save it or to save a file under a different name or in a different directory from the previ ous version you need to use the
86. multi line titles To change the text of data set color code keys select one only data set and enter the text in the Label entry box in the Plotting Attributes control panel To display or hide hkl labels next to data circles on x y z graphs check or uncheck the Include hkl Labels check box in the Plotting Attributes control panel To display or hide axes axis labels the title all the data set keys or cell indications set the appropriate Annotation Options pop ups in the Graph Annotation control panel A gt popup label means that several graphs are selected for editing and that the 300 Cerius Modeling Environment April 1999 Additional information Displaying and editing graphs annotation options differ for those graphs or that no graph is selected Please see the on screen help for details on the functioning of each control in the Graph Annotation and Plotting Attributes control panels Changing graph axes and scale Related information Accessing the tools Changing x and y axes You can scale selected graphs in several ways to aid in viewing their data For example you can change the ranges of the x and y axes scroll along an axis and change the proportions of a graph Selecting graphs Selecting and displaying graphs and data sets Selecting which data sets to display and edit for editing are discussed above Specifying immediate or delayed updates of the graph dis play is presented under S
87. name of your command script file To run Cerius without the graphical interface in foreground mode enter at the system prompt gt cerius2 n o outputfile scriptfile 382 Cerius Modeling Environment April 1999 Managing licenses When to manage licenses Managing licenses where outputfile is the name of the file that you want to send any text output to and scriptfile is the name of your command script file To run Cerius without the graphical interface in foreground mode and send any text output to the shell window rather than to a file enter at the system prompt gt cerius2 n scriptfile where scriptfile is the name of your command script file As an end user you rarely need to be concerned about license management since it is handled automatically after the Cerius software has been installed 2 Some situations exist in which you may want to manage licenses interactively for example Suppose your site has a limited number of licenses and they are all being used by other people If you need a license you may want to determine who the other users are Then you can ask one of them to replace that is check in the license so that you can work Ifyou plan to run along command script you may want to reserve that is check out enough licenses to assure that they are available when needed Important Accessing the tools If you want to run Cerius applications in parallel please see the Ce
88. named in the illustration below Overlay mode tool Grid mode tool Add model space ______ gt Sorting criteria z gt Model name Visibility indicator Scrollbar 7 A Using the model manager z 1_ gt Modell Model ID number Current model indicator ee Delete model space Clear model space a Model count ae Set to visible au Ke ay invisible oe HA Models 1 Model table The model manager is used to view collections of models sort mod els by name and by identity number and discard models from the Visualizer 1 Load the models If Cerius isn t already running type cerius2 in a UNIX shell to start the program 78 Cerius Modeling Environment April 1999 Managing Modelsand More Choose Load Model from the File pulldown menu Use the Load Model control panel to load models from the previous tutorials phenol msi cyclohexane msi and xylene msi The file names without the msi extensions appear in the model manager list in the same order that the files are loaded in Load butane msi and napthalene msi from the Cerius2 Models organics directory There are now five models in the system Each is named and numbered on the model manager list The diamond after the model number is the current model indicator i e the displayed model on which calculations will be performed The current model i
89. numbers and the frame increment Then click the BUILD FRAMES pushbutton in the Ani mation control panel Animating the model Once the desired frames have been built into an animation sequence you can use the Replay Animation controls to animate Cerius Modeling Environment April 1999 241 8 Viewing and Displaying Models Clearing memory Additional information the model by replaying all or specified frames These controls operate similarly to those on a tape recorder or VCR You can use other controls during or before the animation for example you can change the viewing angle Rotating models mag nification Changing the view magnification or display style Atom and bond display styles Animation sequences consume a considerable amount of memory When you have finished with a sequence you should clear the memory buffer in which it is held by clicking the Clear All Frames action button in the Animation control panel Please see the on screen help for details on the functioning of each control in the Animation and Frame Filter control panels Labeling and annotating models Why read this section Finding information Related information Cerius allows you to label atoms according to various properties such as element names atom type charge temperature hybrid ization etc You can also annotate models by adding text and graphical objects such as arrows and boxes In addition the default type of annotati
90. of the Table Properties control panel enter the heading text for the selected row s in the Row Name entry box and assure that the Row Name check box is checked Click the APPLY TO pushbutton Next in the Heading pane of the Table Properties control panel check either or both the Show Row Names and Show Row Num bers check boxes Click the APPLY TO pushbutton Cerius Modeling Environment April1999 331 11 Working with Tables Entering and displaying column headings Specifying banners Additional information You may want to change the width of the heading column Chang ing heading sizes In the Column pane of the Table Properties control panel enter the heading text for the selected column s in the Column Name entry box and assure that the Column Name check box is checked If you want a second line of heading often used to specify the units for the data e g kcal or angstroms enter the text in the Col umn Units entry box and assure that the Column Units check box is checked Click the APPLY TO pushbutton Next in the Heading pane of the Table Properties control panel check one or more of the Show Column Names Show Column Numbers and Show Column Units check boxes Click the APPLY TO pushbutton To display two lines of heading you probably need to increase the height of the heading row Changing heading sizes To prevent a row or column from scrolling off the screen when the rest of a large table is scrol
91. open control panels if you have too many control panels cluttering up your screen Use the File New Session menu item to set all controls to their defaults and remove the models from the model window Reload your caffeine model Or if you want to stop for a while please see Step 13 for exiting Cerius and restarting this tutorial Printing a model If you ve interrupted your tutorial please see Step 13 before start ing this section If you ve deleted caffeine from your Cerius session please reload it see Step 13 if you need instructions You may have to use the file browser in the Load Model control panel to navigate back up to the directory in which you stored caffeine msi If several models are visible make caffeine the only visible and active model by assuring that the visibility controls square blue icons in the model table are toggled off for all other models and on highlighted for caffeine Change the display style from STICK to something else if you pre fer see Step 21 Select the File Print menu item In the Print control panel change the Command to the state ment that you usually use to specify printing to a postscript printer Cerius Modeling Environment April1999 41 2 Introducing C erius An experienced user at your site or your systems administrator should know this command if you don t Either select the PRINT button or change the settings of some of the other
92. panel Identify what type of property is to be mapped by choosing an item from the Attribute popup in the Edit Color Mappings control panel Specify that the property to be mapped will use a color range by setting the Type popup to CONTINUOUS The contents of the bottom of the Edit Color Mappings control panel depend on the value of the Type popup Set the Minimum and Maximum Attribute Values between which the color map s range is to extend Tip Coloring the values within the range For properties that have integer or close to integer values such as the atomic mass set the minimum and maximum values so that they fall about halfway between expected values For example you might set the minimum mass to 0 5 and the maximum to 40 5 if you are modeling a biochemical molecule Decide what part of what color range to apply to the range of mapped property values by choosing the range s name from the Use Range popup and entering the Minimum and Maximum range color entry numbers in the Color Scheme section of the 276 Cerius Modeling Environment April 1999 More colors How to handle outliers Saving a color map Example Additional information Customizing display colors control panel If you want to use the color range in reverse order make the maximum smaller than the minimum If you want for example to create a ternary mapping scheme rather than a full color range or to highlight the outlie
93. panel to access the Lightsource Position control panel where you can change the light from directional to positional and then change its position For example set the X Y and Z values to 1 1 and 10 respectively to place a light in front of the model somewhat to its lower right Click the Spotlight button in the lighting control panel to access the Spotlight Settings control panel where you have additional control over the positions of spotlights positional light sources For example set the Latitude and Longitude controls on this control panel to 5 68 and 174 29 respectively to shine the light back towards the model Narrow the Cutoff to say 20 to make a narrow beam of light Try increasing the Falloff value to smooth the transition from the light to the dark area Iteratively change the Position controls in the Lightsource Posi tion control panel and the Direction controls in the Spotlight Settings control panel so as to for example illuminate a partic ular atom or center the light on the 6 membered ring Click the Attenuation button in the Lighting control panel to access the Lightsource Attenuation control panel Try increas ing the Linear or Quadratic factor to make atoms farther from the lightsource appear dimmer The effect is more apparent if the illuminated part of the model is nearly parallel to the direc tion of the light beam More lights Add a second light source by changing the Light popup in t
94. panel work see How it works or how controls work in general The Cerius2 Interface Editing element and bond attributes Related information You should already know Hement properties What element properties can be edited Cerius allows you to edit the default properties of elements Ele ment properties change how bonds are determined Bond proper ties and adjust the criteria for determining hydrogen bonds Hydrogen bonds Changing the properties of individual selected atoms i e not nec essarily of all atoms of a given element type is covered under Changing atoms and their bonding types Setting temperature factors is discussed under Temperature factors You should have already worked with the types of models and the various application modules that you typically use before decid ing whether and how much you should change the default behav ior of Cerius And of course there is no substitute for chemical knowledge and intuition This section is for experienced Cerius users 2 Element properties are stored within Cerius and used for calcula tions and display attributes These properties include mass van der Waals radius atomic radius covalent radius metallic radius ionicity hydrogen bonding nature and display color Cerius ele Cerius Modeling Environment April 1999 179 5 Building Models Editing element properties Additional information Mixture elements Dummy atoms
95. primary command Utility Generated internally within Cerius for defining the environment in which Cerius and its application modules are to run for example the commands generated when command tracing is turned on or off Select the Utilities Command Tracing menu item in the main Visualizer control panel to access the Command Tracing control panel To specify the level see Levels of commands of commands to trace check one or more of the Activate Command Tracing check boxes To turn on or off tracing of primary commands you can also check the Activate command tracing check box in the Customize Environment control panel Accessing the tools The commands are sent to the text window and or a file as specified in the Command Tracing control panel see Where to send the commands 378 Cerius Modeling Environment April 1999 Where to send the com mands Changing command tracing Examining most recent commands Additional information Controlling Cerus from scripts To display the traced commands in the text window check the Text Window check box To log the traced commands in a file check the Trace File check box and if desired enter a filename in the Trace File entry box To stop command tracing or change the level of commands to trace uncheck the relevant check boxes in the Command Tracing control panel To print the most recent primary and utility commands in the text window enter the comman
96. ring structure Cerius often offers several ways of accomplishing the same activity allowing you to use whatever method you find convenient We ll dem onstrate two different ways of adding groups of atoms to a model But first we ll show a different way of changing the atom that you ll be sketching with Click in the Sketch with text entry box The N becomes highlighted Anything you type in the box will now replace the N Cerius Modeling Environment April1999 13 2 Introducing C erius Type a C in the Sketch with text entry box and either press lt Enter gt on your keyboard or click anywhere else on the con trol panel In other words Enter C in the Sketch with text entry box Click the bottom carbon in the 6 membered ring then click below that carbon This adds a carbon which will become a methyl group when you cor rect the hydrogens later You may want to look at the picture of a complete caffeine model under Cleaning up the conformation for help in sketching your model Here s another way of adding a methyl group Click the Templates button in the Sketcher control panel The Templates button looks like Clicking the Templates button causes the Sketcher Template con trol panel to appear This control panel contains a file browser that 14 Cerius Modeling Environment April 1999 Building a model caffeine allows you to navigate among di
97. see Running Cerius2 without the graphical interface If you have certain tasks that you always or often perform when you start a Cerius session you can record them in a command script file and then have Cerius automatically perform these tasks from the script either immediately this section or when you request it Playing back scripts and log files Then you can pro ceed with additional tasks using the graphical interface If you have repetitive routine calculations or other tasks that can be performed without the graphical interface you can record these tasks ina command script file Then you can run Cerius in a com pletely automated way in either the foreground or background without your interacting with the graphical interface at all To run Cerius from a command script with the graphical interface and have it immediately and automatically process a certain com mand script move cd to a directory containing an initialization script then simply start Cerius as usual An initialization script is simply an ordinary command script file that you have saved with the filename cerius2 ini see Recording commands Cerius Modeling Environment April 1999 381 13 Scripts and Licensing Starting Cerius with a specified script Running Cerius without the graphical interface To set up different initialization scripts for use when you run Cerius for different purposes or projects simply create separate directo
98. shows a model table with one current model that is implicitly visible ID 8 several visible models IDs 4 5 7 8 several invisible models IDs 6 9 10 several selected model 204 Cerius Modeling Environment April 1999 Renaming models Example Handling multiple models spaces IDs 5 6 9 and one model that is being renamed ID 10 with scrolling needed to see the whole list 4 lt c60 7 benzene Sd 8 butane ji 10 Se Newly created empty model spaces are given the name Model where is the serial ID number of the model space Models loaded from disk into an empty model space are given a name based on the structure file name If a model has or is given the same name as an existing model the name is suffixed with _1 _2 _3 etc You can rename models by clicking the existing name then typing anew one and pressing lt Enter gt or clicking somewhere else on a control panel An example of renaming a model is given under Reading in more models Sorting model table entries Sorting criteria To assist you in browsing through the models stored in the model table the model manager provides four sort criteria controls These controls enable you to sort model table entries according to model ID number current model status model name or visibility To select the criteria by which models in the model table are sorted select the appropriate control The ID tool Sort model table entries i
99. tables contarniig both data and models and can modify tables created by Cerius application module This section provides basic information on working with Cerius tables This section explains Following an introduction to Cerius tables Introduction to Cerius2 tables this section contains information on Managing and editing tables Table style and display Values and mathematical expressions Models in tables Grouping table information Searching for information in a table Viewing subsets of a table Sorting table information Graphing table information Exporting table information Table 11 Finding information about tables If you want to know about Read Finding the Tables module Accessing the tools Parts of the table window The table window Making a table curent Specifying the current table Attaching control panels to tables Keeping track of the current table Moving the cursorina table Selecting a cell Cerius Modeling Environment April 1999 311 11 Working with Tables Table 11 Finding information about tables If you wantto know about Cursor wrapping The current cell Default cell format Data type and display format Entering data into or editing a cell Recording your edits Cutting and pasting values Working with rowsand columns Applying equations to cellsand col umns Relation between valuesand expres sions Components to include in expressions Getting models into a table Ref
100. text lines that can be used for whatever purpose you want Cerius leaves them blank These are followed by records that define element type bond length bond angle torsion angle connectivity and charge for each atom The three geometry parameters bond length angle and torsion angle are followed by a flag that can be 0 or 1 If the flag is 0 the geometric variable is fixed if 1 it will be optimized Cerius Modeling Environment April 1999 425 D File Formats MOPAC files consist of three standard records plus one record for each atom These records are described in terms of FORTRAN edit descriptors in the following table Record Format Storage 1 Free format space Keywords Reserved forMOPAC orAMPAC keywords separated text 2 A free format text Title 1 A line of optional user specified text 3 A free format text Title 2 A further line of optional user specified text 4on A F l F 1 F 1 3l F Element type in free format length flag angle flag tor one peratom sion angle flag connectivity atom numbers charge Bond lengths are specified in angstroms and angles in degrees Flags in record 4 onwards can take values of 0 or 1 0 The preceding geometric variable is fixed 1 The preceding geometric variable will be optimized The Brookhaven Protein Data Bank PDB structure file format can be used to save both 3D and nonperiodic structures and is widely recognized by molecular model
101. the automatically interpolated colors that lie between critical entries The number of entries means the number of noncritical entries The greater the number of entries the smoother the color inter polation in the color range In editing or constructing color ranges you can change the color definition of each critical entry the number of critical entries the position within the range of each critical entry and the number of noncritical entries between each two sequential critical entries You can display a color range in the model window by selecting the Utilities Customize Color Ranges menu item from the main Visualizer control panel to access the Edit Color Ranges con trol panel Then choose a color range from the Color Range popup and check the Show Color Range check box The numbers of the critical entries are displayed alongside the crit ical entries in the displayed range facilitating their identification Cerius Modeling Environment April 1999 271 9 Enhancing Model Display Selecting colors from ranges The numbers of the critical entries are displayed in a list box under Edit Critical Color Entries in the Edit Color Ranges control panel whether or not you display a color range To apply a color from a range to an object in the model window see Choosing colors from a color range You can select a color from a color range by specifying the number of the entry whether critical or noncritical that corre
102. the final color You cannot how ever change the name used for that color To return a single pen color to its default value choose its name from the Pen popup and click the Reset Pen to Default action but ton To return all pen colors to their defaults click the Reset all to Default action button Cerius Modeling Environment April 1999 269 9 Enhancing Model Display Tip You can also define a new set of pen colors in the same way as color ranges are created Color ranges Additional information Please see the on screen help for details on the functioning of each control in the Pen Colors control panel Color ranges A color range is a set of colors that you apply or that Cerius auto matically applies to various properties and data values You can create and edit color ranges Uses of color ranges Customized color ranges are useful for tasks such as Highlighting an important point on a graph Using a colored contour line within a greyscale diffraction pat tern to highlight an interesting point Appropriately changing all the colors used in a model to improve its visibility after the background color of the model window is changed Changing a greyscale plot to a monochromatic colored plot You can edit all the color ranges that are supplied with Cerius Table 9 as well as create your own color ranges Table 9 Some color ranges supplied in C erius and their typical uses Color range
103. to change the display style to Ball The atoms are displayed as spheres By default they are filled to 0 7 of their van der Waals radii Troubleshooting If some of the atoms stayed in stick display If not all the atoms appear in Ball display You may have inadvertently selected some of the atoms in the model window If any atoms were in a selected state then only those selected atoms will appear as balls To correct this click in some empty space in the model window this deselects any previously selected atoms Then reselect Ball from the Display Style popup Select Stick from the Display Style popup menu The model returns to stick display where all bonds drawn as lines B Viewing and labeling a model The following steps show you how to rotate and translate the trim ethylbenzene model You also learn how to label atoms in the model by element name 1 Manipulate the model s presentation using the mouse Rotate the model by placing the cursor over the model win dow and then dragging while holding down the right mouse button Familiarize yourself with the action of the mouse Cerius Modeling Environment April 1999 53 3 Tutorials If the cursor is near the center of the screen it rotates the model about an axis in the plane of the screen and perpendicular to the direction in which you drag If the cursor is towards the edge of the screen it rotates the model around an ax
104. to perform various activities when the cursor is over Cerius Modeling Environment April1999 411 C Mouse and Keyboard Actions Graph window Model window Table window Graph window Table 34 Manipulating graph in graph window with keyboard Keys Action lt Home gt Retum magnification or scrolling to its original value Model window Table 35 Key combinations that mimic menu items in main contol panel Keys Menu item lt td gt Delete gt Edit Delete lt Alt gt a Edit Select All lt Alt gt c Edit Copy lt Alt gt Edit Duplicate lt Alt gt o View Set Origin lt Alt gt r View Reset View lt Alt gt t View Center lt Alt gt v Edit Paste lt Alt gt w View Fill Window lt Alt gt x Edit Cut Table window 412 Cerius Modeling Environment April 1999 Keyboard shortcuts Table 36 Manipulating model in model window with keyboard Use keys on an extended keyboard not on a numeric keypad Keys lt 1 gt lt 2 gt lt F3 gt lt 4 gt lt 5 gt lt F10 gt lt gt lt gt lt Home gt lt End gt lt gt lt gt lt l gt lt gt Action Display function key help Toggle between full screen and nomal model display Toggle between orthographic and perspective display projection Projection Toggle between full screen stereo and normal model display In stereo mode toggle between Crystaleyes and stereo pair mode Stereo viewing On 8 bit machines toggle between
105. ture to an energy minimum or a transition state with one of the quantum applications You can also use the quantum applications to enforce space group symmetry Documentation for these mod ules is supplied separately Advanced building and editing Why read this section This section tells you where to access some building and editing controls such as editing atom attributes and changing defaults and preferences that are not as commonly used as those discussed earlier in this section It contains information on Editing element and bond attributes Introducing substitutional disorder Introducing positional disorder Temperature factors Control of the model cleaning function 178 Cerius Modeling Environment April 1999 Related information You should already know Advanced building and editing Basic building tasks are presented under Basic building and basic editing tasks under Basic editing Displaying labels and other information about atoms in a model is presented under Labels Saving nondefault settings for later use is described under Working with Cerius2 sessions You need to know how to select atoms in your model Selecting atoms and groups of atoms so you can edit them You also of course need to know how to build Basic building and edit Basic editing a model and or load a model from a file Loading model structure files You may want to review the basics of how the controls in the Sketcher control
106. types Optionally bonding connectivity higher order bonds crystal unit cell parameters space group and atomic charge information can also be stored The default file extension for CSSR files is cssr although for 3D structures fcssr is some times used to indicate that fractional coordinates have been used CSSR files consist of four standard records plus one for each atom These records are described in terms of FORTRAN edit descriptors in the table below Stores Cell dimensions Contains the length of the three cell parameters a b and c in angstroms Cellanglesand space group Cellangles a b g in degrees space group number space group name Title numberof atomsand coordinate system Number of atoms stored coordinate Fie flag O fractional coordinates 1 orthog onal coordinates in first title Second title A line of text that can be used to describe the file read on input but otherwise unused Atom specific information Atom serial number atom name x y Z coordinates bonding connectivities max 8 charge Note The atom name isa concatenation of the elementsymboland the atom serial number Cerius Modeling Environment April 1999 423 D File Formats ICSD read only Cerius provides read only support for Inorganic Crystal Struc ture Database ICSD format files default file extension icsd Cerius reads element types bonding atom coordinates and crys tal unit cell parameters Sy
107. windows to a single icon on your desktop Cerius Modeling Environment April 1999 133 4 The Cerius Interface The menu bar The menu bar is found at the top of the main control panel The items on the menu bar provide click and drag access to related sets of controls File Access to session control output and file operations These include working with Cerius sessions loading and sav ing structure files and printing See Managing Models and Ses sions Printing models and graphs Edit Access to atom selection and editing tools See Selecting atoms and groups of atoms and Basic editing Build Access to the Visualizer s general model building including the 3D Sketcher and attribute editing tools See Building Models Builder modules that provide additional spe cialized model building functionality are accessed from the deck of cards menu and are described in Cerius Builders View Access to tools that enable you to manipulate the view of models in the model window as well as to produce high quality displays and renderings of those models See Viewing and Displaying Models and Enhancing Model Display Move Access to tools that enable you to alter the 3D geome try of models by moving atoms See Translating and rotating atoms and Aligning and positioning atoms Geometry Access to geometry analysis tools which enable you to examine the 3D structure of models See Geometry Anal ysis
108. with an script Cerius is started automatic script mixture ele Special elements whose propertiesare definable Mixture elements ments asproportional mixtures of those of real elements model manager Set of toolsin the main control panel formanaging Using the main control models and model spaces panel modelspace A virtual space inthe model managerenviron Creating clearing and ment that may or may not contain a model deleting model spaces pen colors Individually defined drawing colors Creating and editing anew color range projection Representation of linearperspective Superimposing models rendering The production of high quality 3D images Rendering and ray tracing residue ID Alphanumeric representation of the location of a residue within a sequence residue type Standard chemical name foran amino acid resi due session Lasts from when you start or reinitialize C erus until Working with Cerius2 ses you quit or reinitialize C erius sions Cerius Modeling Environment April 1999 403 B Definitions word specular light temperature factors thermal ellip soids value Visualizer additional meaning information Highlights reflected from an object Concepts Used to describe the effect of thermal vibration on Temperature factors crystal structures Used to represent the thermal motion of atoms Thermal ellipsoids The information actually displayed ina table cell Applying mathematical expres
109. you want to use set the appropriate controls in the area of the control panel below the Format popup The controls that are available in this section depend on which format you choose Enter a filename in the entry box and click the EXPORT pushbut ton to save your file Use of the file selection list box and other file selector controls to navigate the directory structure is presented in detail under Find ing model file s Creating your own directories or subdirectories is described under Making custom directories Please see the on screen help for details on the functioning of each control in the Export Table control panel 366 Cerius Modeling Environment April 1999 Exporting table information Cerius Modeling Environment April 1999 367 11 Working with Tables 368 Cerius Modeling Environment April 1999 6 Working with Isosurfaces You should already know Accessing the tools Grid properties are generated by a number of Cerius application modules e g ADF MOPAC DMOL3 Free_Volume as well as many third party applications A grid specifies a volumetric prop erty as a three dimensional array encompassing a molecular model Typical grid properties are molecular orbitals electron density electrostatic potential and molecule accessible surface The Isosurfaces application provides generic capabilities for the analysis of such grids via the construction of either a 3D isosurface or a 2D slice plane
110. your model by setting Y and Z to 0 0 and X to a number in ang stroms beyond the right side of your model say 10 A for a small molecule model This is equivalent to setting Latitude to 0 0 Longitude to 90 and the Radius in angstroms to the value used for X Position the light in the lower right forward quadrant of the scene by setting Latitude to about 30 Longitude to about 80 and Radius as needed to produce the desired effect perhaps 10 A for a small molecule model Provide backlighting by increasing the absolute Longitude beyond 90 or 90 or by using a negative value for Z Illuminate at the position of an atom by pressing lt Shift gt on the keyboard and clicking the atom with the right mouse button to obtain an information window that includes its Cartesian coor dinates this information is also printed in the text window Enter these values as the X Y and Z values You can then pull the light away from the model by increasing the Radius To help in assessing the size of your viewing area you can select the View Options menu item to show a scale bar in the model window Cerius Modeling Environment April 1999 285 9 Enhancing Model Display Spotights Positional lights can be made into spotlights which can highlight various features by illuminating only a small part of your model with a cone of light Directional lights cannot become spotlights since they are located at infinit
111. your own machine or an accessible machine on your in house network Either you or you system administrator should have done this with the help of the Cerius Installation and Administration Guide You need to know how to log in to your machine how to get around in your directory structure and the basics of managing Cerius Modeling Environment April1999 5 2 Introducing C erius your file system and working with your machine s user envi ronment see for example Todino amp Strang 1990 You need a home directory in which you have write permission and can create subdirectories You need to know how to start up Cerius on your machine Whoever installed Cerius at your site can tell you how to start it If their instructions differ from those given under Starting Cerius2 please follow the instructions for starting Cerius at your site Layout of this section In general activities that you must perform if you want this tutorial to work as designed are contained in boxes like this Optional activities are in plain text not in boxes Explanations of what you are doing are in italics Note If you want to perform only some of the optional activities or are interrupted and need to redo some of the initial activities you need read only the boxed information Additional information Detailed information on how to carry out the activities introduced in this section as well as other activities is
112. 135 The model manager 1 0 0 cece ee ees 136 Deck of cards menu n u ee 136 Controls and control panels 2 0 0 6c eee eens 138 Types of controls 2 0 eee eee 140 Managing control panels 0 6 c eee eee 141 Information SourceS a nus anann eee 142 On screen Delp ereu saaa aaan EE a a S 142 Menu card searching 1 0 6 6 cece eee eae 142 Messages and status information 142 Other Windows 0 0 c ccs 144 Building Models 145 Basic building degant a stien mnia E EE RA ERE 146 Starting to construct a new model 147 Strategy cne a a Sa ase ee o A 147 The 3D Sketcher 0 0 cece eee 149 Other basic building tools 54 150 Adding atoms and bonds 0 000 esas 151 Selecting the element ype Gayle ances chaae aaa sa tree 151 Adding atoms and single bonds 152 Adding templates groups of atoms 154 Selecting templates 00 cece eee 154 Adding templates toa model 155 Custom templates 0 00 cece eee 155 Fusing and connecting fragments 156 Adding hydrogens 0 ccc c eee ees 157 Selecting atoms and groups of atoms 0 000 158 Selecting and deselecting individual atoms 159 Selecting atoms in several models 160 Selecting and deselecting collections of atoms 161 Selecting according to properties 161 Defining and selecting groups 4 162 Customize
113. 169 hydrogen bonds acceptors 184 calculating 183 184 color 183 criteria 183 deleting 171 183 442 Cerius Modeling Environment April 1999 donors 184 editing 183 Hydrogen tool 158 hydrogens adding 153 157 adjusting 157 and hybridization 158 correcting 19 199 deleting 157 hiding 255 number 158 ICSD file format 424 Import Table control panel 319 320 Import TBL File control panel 296 297 integers 330 interfaces 191 interrupting processes 143 introduction to Cerius2 5 inversion angles measuring 221 Inversion tool 221 Invert tool 174 isosurfaces 369 see also surfaces ISOSURFACES card 369 ISOTROPIC 243 isotropic temperature factor 187 italic type meaning 3 4 K keyboard accelerators 135 shortcuts 135 407 shortcuts on screen table 45 L label popup 23 label properties 243 labeled buttons 140 labeling a model 23 243 labels adding changing removing 243 atoms 243 bonds 244 lanthanides 182 LEED RHEED reflections 295 License Management control panel 383 384 licenses checked out 384 features 384 floating 384 managing 383 module specific 384 number 384 reserving 384 returning 384 token 384 light attenuation 280 287 color 280 direction 284 location 285 position 280 285 reflected 280 scattered 280 lighting 43 ambient 280 282 283 brightness 282 283 287 color 43 282 283 concepts 280 diffuse 280 283 directional 44 280 284 discrete sources 283 function of distance 287 general
114. 280 global 280 highlights 280 inside and outside 282 latitude 280 light positions 44 longitude 280 multiple sources 44 OpenGL needed 279 positional 44 280 285 specular 280 283 spotlights 44 286 two sided 282 white 282 283 Lighting control panel 282 283 Lightsource Attenuation control panel 287 Lightsource Colors control panel 283 Cerius Modeling Environment April 1999 443 M Lightsource Position control panel 284 285 286 Load Connolly Surface control panel 225 226 Load Graphs control panel 296 297 Load Model control panel 196 199 Load Preferences control panel 199 Load Session control panel 213 local energy minimum 185 localhost 386 Lowenstein s rule 184 M MACCS Molfile file format 415 424 magnification 234 main control panel 128 illustration 132 mapping properties onto surfaces 371 MASS 243 Match Atoms control panel 240 Match Models control panel 239 mathematical expressions 333 binary mathematical operators 339 binary model operators 345 binary text operators 348 command operators 348 constants 342 cross references 343 division by zero 339 entering in tables 335 entering once 336 errors 339 model calculations 344 model calculations automated 351 operators 337 order of precedence 339 parentheses 339 physical constants 342 references to other cells 343 removing 337 statistical operators 340 statistical transformations 341 table operators 348 trigonometric operators 341 unary math
115. 435 mass 181 moving 175 name 154 181 named collections 162 named groups 162 nonstandard using 32 occupancy 181 pasting 207 pasting to or from nonCerius2 applications positions 153 176 210 properties 179 181 244 267 275 276 397 properties querying 164 querying current properties 244 randomizing positions 185 selecting 25 158 specifying coordinate positions 153 thermal motion 254 translating 175 background color 45 268 backlighting 284 285 balloon help 397 beeper 397 bell 397 BGF file format 419 blend transparency defined 279 bold type meaning 4 Bond Calculation Preferences control panel 182 Bond Geometry control panel 172 173 174 Bond Type Calculation Prefs control panel 182 bonding information 210 bonds and atomic radii 182 automatic placement between unbonded atoms 181 calculating 181 changing the type 17 168 colors 249 controlling lengths 171 181 covalent 182 criteria 181 182 defaults 181 deleting 170 determining the type 182 display style 249 general 182 inhibiting creation of 182 Kekule 250 labeling 244 line width 258 measuring lengths 172 219 351 missin 189 multiple 250 partial double 250 preferences 181 resonant 250 Slater 182 png 181 specifying type 153 R border mode tool 38 branched chains building 153 building a model 8 approaches 148 beginning 152 comprehensive description 146 dashed line 12 152 mistakes 13 strategies 147 template
116. 6 145 146 calculations 351 centering 237 color 280 283 composite 206 continuous rotation 234 copying 207 copying parts to another model space 207 copying to another model space 40 206 cross sections 256 depth cueing 257 display 203 204 263 docking 237 duplicating all or part of 207 editing 164 labeling 243 lighting 279 loading 35 45 196 198 loading several 198 213 magnification 234 managing 199 matching atoms 239 measuring 218 351 more than one 35 199 moving to another model space 207 orienting 234 projection 257 renaming 35 205 rendering 287 resetting the view 236 rotating 233 238 saving 210 saving all 212 saving part of 210 selecting 45 161 203 serial numbers 203 size on screen 234 spotlighting 283 286 structure trace 255 superimposing 239 supplied by MSI 199 tables 350 351 transferring to other programs 208 translating 232 238 viewing 203 viewing angle 233 views 240 visibility 203 270 zooming 234 modules accessing 137 other builders 191 Molecular Simulations Inc contacting 46 customer support 46 email 46 website 46 MolEN file format 425 molybdates 253 MOPAC file format 425 426 More Psycho Options control panel 289 mouse controls button and key combinations 407 buttons 131 changing function 233 on screen table 45 MSF file format 418 MSI file format 416 Multiple Color Mappings control panel 267 Cerius Modeling Environment April 1999 445 N NAME 243 Neider J 281
117. 6 Twist tool 173 typewriter font 4 typographical conventions 3 6 U uncheck definition 132 UNDO button 150 154 248 UNIX shell commands entering 130 V valence satisfaction 182 van der Waals radius 179 252 253 Vector Preferences control panel 226 Vector Properties control panel 226 vibrations atomic 186 254 view angle 244 position 282 scale 285 View Options control panel 233 234 235 245 Viewing Dials control panel 232 234 235 236 views depth 256 mono 290 saving and retrieving 240 stereo 289 Visualizer module 23 127 W warning messages 142 window manager controls 133 windows iconifying 129 managing 45 stowing 129 Woo M 399 X xpsview 261 X ray scattering 187 first order amplitude 187 Z z clipping 256 Z Clipping control panel 256 zeolites 184 253 450 Cerius Modeling Environment April 1999
118. 65 9 Enhancing Model Display Mixing your own colors Choosing colors from a color range Reverting to default colors popup You can also access this control panel from the More Colors pushbutton on the Annotation control panel next paragraph or Select the Build Annotation menu item to access the Anno tation control panel then choose a color from the colors popup to the right of the Line tool You can edit the pen colors to make your own set of predefined colors see Drawing colors To mix your own colors for selected atom s or other object s select the View Colors menu item to access the Color Selected Objects control panel Use the red green and blue sliders or the entry boxes below them to set the proportions of red green and blue in the final color To choose colors for selected atom s or other object s from a range of colors select the View Colors menu item to access the Color Selected Objects control panel Click the Color Ranges pushbutton to access the Color by Range control panel Choose any range from the list and check the Show Color Range check box if you want to display the color range with color num bers in the model display window Then enter the number of the desired color in the Use color num ber entry box You can edit color ranges to change them or create additional color ranges see Color ranges To set selected atom s or object s back to their default
119. 7 C Mouse and Keyboard Actions Table window This section summarizes mouse activities only when the cursor is in selection mode see Selecting and deselecting individual atoms Equivalent information for other modes such as various measur ing modes is contained in the relevant sections of this documenta tion since other modes are generally specific to certain types of tasks Contol panels Any contol Table 27 Mouse actions that work when cursor over almost any contol Button Key Operation Action wait Allow balloon help to appear v click Activate or operate a control Vv click Obtain help ona control Mhe check mark indicates which mouse button to press File browser Table 28 Selecting files in file browser in any contol panel containing one Button Key Operation Action v click Select only one file v drag Select only a range of files y double click Load the file v lt Shift gt click Select from the last selection through the file clicked upon y lt Ctri gt click Select deselect the clicked file no change to otherselections v lt t gt drag Selecta range of files no change to other selections 408 Cerius Modeling Environment April 1999 Mouse actions Mhe check mark indicates which mouse button to press Model table Table 29 Selecting models in main contol panel s model table Button Vv SISINSINIS v
120. 8 close button 22 141 close contacts 222 exclusions 222 Close Contacts control panel 222 223 color 304 any object 265 atoms 29 background 45 268 bonds 249 by properties 267 Cerius2 interface 394 control panels 394 custom 268 default 266 267 269 defining 266 269 drawing 269 elements 265 graphs 303 pen 269 predefined 269 selected atoms 265 standard 269 Color by Range control panel 266 color map defined 274 color maps 267 applying 275 attributes 275 276 binary 275 continuous 276 creating 275 276 defining 275 276 deleting 278 editing 275 276 278 loading 278 multiple 267 on off properties 275 outliers 277 property types 275 276 renaming 278 saving 276 277 selecting 278 sequence 267 ternary 277 uses 274 color range defined 270 color ranges 266 color gradation 272 concepts 271 creating 272 critical entries 271 272 Cerius Modeling Environment April 1999 437 critical entries adding 272 critical entries positions 273 critical entries removing 274 defining 272 deleting 274 displaying 266 271 272 editing 272 273 graphs 304 interpolated colors 271 interpolation smoothness 271 loading 273 noncritical entries 271 number of colors 272 renaming 274 saving 273 selecting 273 selecting colors 272 supplied with Cerius2 270 273 uses 270 Color Selected Objects control panel 265 266 267 268 command scripts comments 377 controlling Cerius2 379 enhancing 380 ini
121. Build in the menu bar Press and hold down the left mouse button 8 Cerius Modeling Environment April 1999 Building a model caffeine A list of menu items or pulldown menu appears Continue to hold the left mouse button down use the mouse to drag the cursor downwards and release the mouse button over the 3D Sketcher item in the list In other words I Select the Build 3D Sketcher menu item A window labeled Sketcher appears This control panel contains basic model building tools 5 Sketching the ring system of caffeine You will not necessarily build caffeine in the quickest possible way since we want to show how several different sketcher tools work Locate the template tool in the Sketcher control panel It is labeled phenyl since a phenyl ring is the default template The template tool looks like Cerius Modeling Environment April1999 9 2 Introducing C erius Use the mouse to move the cursor over the template tool and click once with the left mouse button In other words Click the template tool Always use the left mouse button to click items unless otherwise indicated The phenyl template tool changes color indicating that it is active and if you move the cursor into the large window you will see that the cursor has changed to a T shape Move the cursor into the large window labelled Cerius2 Mod els Definition This is ca
122. CALCULATE pushbutton to calculate and display a Connolly surface Once you have calculated and displayed a surface for all or selected atoms in a model you can toggle the display of that sur face by using the Hide check box Surfaces can take up large amounts of memory Therefore it is a good idea to delete them when they are no longer required Then recalculation or reloading if you saved the surface see Saving and loading Connolly surfaces is required to display them again A Connolly surface is not part of the fragment itself So if you delete all or part of the fragment the surface remains unchanged until you recalculate or delete it Before a new surface is calculated and displayed the existing sur face is deleted If you want to view two different Connolly surfaces on a model copy the model to a second model space Copying whole models from one model space to another generate the second surface for the copy change its color and then display both models together using the overlay display mode Controlling model visibil ity and the display mode Connolly surfaces can be saved and loaded using the Save Sur face and Load Surface pushbuttons respectively on the Con nolly Surfaces control panel The file format is compatible with equivalent files generated in POLYGRAF and has a default exten sion of dot Note that the file saves only the position and color of the dots that make up the surface the atomic pos
123. Cerius Modeling Environment April 1999 Last Full Revision J uly 1998 jors oa grr moe 9685 Scranton Road San Diego CA 92121 3752 619 458 9990 Fax 619 458 0136 Copyright This document is copyright 1997 1998 1999 Molecular Simulations Inc a division of Phar macopeia Inc All rights reserved Except as permitted under the United States Copyright Act of 1976 no part of this publication may be reproduced or distributed in any form or by any means or stored in a database retrieval system without the prior written permission of Molecular Simulations Inc The software described in this document is furnished under a license and may be used or copied only in accordance with the terms of such license Restricted Rights Legend Use duplication or disclosure by the Government is subject to restrictions as in subpara graph c 1 ii of the Rights in Technical Data and Computer Software clause at DFAR 252 227 7013 or subparagraphs c 1 and 2 of the Commercial Computer Software Restricted Rights clause at FAR 52 227 19 as applicable and any successor rules and regula tions Trademark Acknowledgments Catalyst Cerius Discover Insight II and QUANTA are registered trademarks of Molecular Simulations Inc Biograf Biosym Cerius CHARMm Open Force Field NMReraf Polygraf QMW Quantum Mechanics Workbench WebLab and the Biosym MSI and Molecular Sim ulations marks are trademarks of Molecular Simulations In
124. Cerius Modeling Environment April 1999 Command line Additional information Advanced building and editing With this control panel you can Select ISOTROPIC or ANISOTROPIC to specify whether iso tropic or anisotropic temperature factors will be used in any rel evant calculation involving the atom to be added Select the format to be used i e Biso or Uiso for isotropic tem perature factors and Uj Bj or Bj for anisotropic temperature factors see Table 3 Enter the value of the isotropic temperature factor or the values for the anisotropic temperature factors The six anisotropic temperature factors are entered as a matrix U11 U12 U13 U22 U23 U33 The selected specifications are applied when you add the atom with the Add Atom control panel Precise positioning of atoms dur ing building If you specify the anisotropic temperature factors from the com mand line you should enter them in the order 1 1 2 2 3 3 1 2 2 3 1 3 Please see the on screen help for details on the functioning of each control in the Added Atom Temperature Factors control panel Editing temperature factors The temperature factors of existing atoms can be edited Select the Build Edit Atoms menu item to access the Edit Selected Atoms control panel In this control panel click the Temperature Fac tors pushbutton to access the Edit Temperature Factors control panel With this control panel you can Select the forma
125. Cerius does not find an MSIguirc subdirectory in the directory in which you start it it looks for an MSIguirc subdirectory in your home directory Please see the on screen help for details on the functioning of each control in the Customize Menu Deck control panel Contol panel management Accessing the tools Reopening control panels Closing control panels In addition to basic control panel management as presented under Managing control panels Cerius offers additional functions for dis playing closing and reorganizing open control panels You can also specify that certain panels be displayed automatically whenever you start Cerius Select the Utilities Panel Manager menu item in the main Visu alizer control panel to access the Panel Manager control panel All control panels that are currently open or were open at some time during the current Cerius run are considered active In addi tion selected control panels can be marked so as to be considered active in subsequent Cerius sessions even without being manu ally opened first see Saving control panel configuration Their names appear in the Active Control Panels list box To perform one of the tasks listed here select one or more of the active control panels by clicking its name in this list Selected con trol panel names become highlighted Deselect a control panel by clicking a highlighted name again To open or reopen selected active control pane
126. Examples of expressions including statistical transformations are normalize col 1 scale col TG Statistical transformations should be used only in column expres sions not cell expressions The columns referred to see To col umns in this example all contain numerical values Table 15 Statistical transformations in Cerius table expressions Operator Retums Description meancenter number Transform a data set that its mean is 0 0 normalize number Transom a data set so that itsmean is 0 0 and its standard deviation is 1 0 scale number Uniformly map a data set onto the range 0 0 to 1 0 Trigonometric operators Trigonometric operators Table 16 take one argument that must evaluate to a number Examples of expressions including trigonometric operators are sind col 5 tan sqrt abs col 5 col 6 Cerius Modeling Environment April 1999 341 11 Working with Tables The column references see To columns in this example all eval uate to numbers Table 16 Tigonometic operators in Cerius table expressions Operator Retums Description sin number Sine radians cos number Cosine radians tan number Tangent radians asin number Arcsine radians acos number Arccosine radians atan number Arctangent radians sind number Sine degrees cosd number Cosine degrees tand number Tangent degrees asind number Arcsine degrees acosd number Arccosine degrees atand number Arctangen
127. In part E page 108 you deleted all the graphs from the Gallery Manager by resetting the Graphs card In the following steps you learn how to selectively remove graphs from the gallery There is another version of the Emix Fit graph saved in the file Cerius2 Resources EXAMPLES data EM_PM_Emix grf Here you load this graph to illustrate the usefulness of the Keep Same and Data Placement options of the Graphs Expert Functions control panel In this exercise you load the second version from file but in practice it will usually be a Cerius module that creates a new ver sion of a graph and pipes it into Graphs However the principle is the same regardless of whether the graph is loaded or piped The Data Placement control lets you decide how to treat new versions of the same graph The Keep Same controls let you apply the graph formatting that you ve specified for one graph to subsequent ver sions of the graph 110 Cerius Modeling Environment April 1999 Managing and Modifying Graphs 1 Create a User graph Open the Gallery Manager control panel by choosing Gal lery gt Manager from the Graphs card Create a new User Graph by checking the third empty Display box in the Graph Chooser list box This causes the list box to update with the name User Graph v1 and an empty set of axes appears in the graph window Next you copy a dataset from the Thermodynamics graph to the new user graph Be sure that the
128. Interface Command logging and scripting Command logging and scripting utilities enable you to record Cerius commands into script files and play them back Playing back scripts and log files at a later time Finding information This section includes information on Recording commands Command tracing Recording commands If you want to understand the course of all or part of a Cerius ses sion you can examine files containing logged commands These files form basic command scripts Command scripts can be played back later Playing back scripts and log files unmodified to repeat a previous session Alternatively you can supplement a command script with Tool Command Lan guage Tcl statements to produce responsive program like scripts that can be used to drive Cerius and its applications Related information To learn more about using Tel to enhance script files see Cerius Command Script Guide as well as information in the documenta tion and support areas of our website 376 Cerius Modeling Environment April 1999 How it works Accessing the tools Recording commands Managing command logs Command logging and scripting http www msi com doc http www msi com support During every Cerius session generated commands are continu ously logged to a file named RUN LOG This continuous log file provides a record of the modeling activity that took place in a Cerius session The RUN LOG fil
129. JUST button on the Sketcher menu to auto matically add hydrogens to satisfy the oxygen valences This produces five or six water molecules D Simulating the behavior of the gluc ose water system 1 Identify the atom types Return to the OFF SETUP card deck and open the Force field Atom Typing menu select Typing Atoms on the OPEN FORCEFIELD card Calculate the atom types using typing rules This identifies the atom types in the water molecules and assigns appro priate partial charges You can select CHARGES from the Atom labelling popup menu to view these charges Change back to NO LABEL before continuing 122 Cerius Modeling Environment April 1999 Basic Molecular Simulation Minimization amp Dynamics Before carrying out a molecular dynamics simulation it is always wise to run a few steps of molecular mechanics minimization to relax any hot spots Select the MINIMIZER card from the OFF METHODS card deck Open the Energy Minimization card by selecting Run from this card Reduce the Maximum Number of Interactions to 200 and Minimize the Energy The most significant interactions between the glucose molecule and the surrounding water will be hydrogen bonds The PCFF forcefield does not contain an explicit hydrogen bond term but correctly models hydro gen bonding as a result of electrostatic and van der Waals interactions between non bonded atoms You can use the Edit H b
130. New Session and selecting the Confirm button on the Re initialize dia log box Re initialization resets all the Cerius control panels to their original defaults Alternatively if you want to stop now Choose File Exit to quit from Cerius and select the Exit button on the Exit Option dialog box Review In this tutorial you learned how to d Sketch atoms L1 Move and delete atoms Cerius Modeling Environment April 1999 75 3 Tutorials T Edit atom and bond types Q Edit bond angles and lengths QO Adjust hydrogens in a model 2 Use the template tool T Clean a model QO Save a model to file You may now want to learn more about the Sketcher by practicing what you have learned by sketching some models of your choosing reading the Basic building section in the Building Models chapter of the Cerius Modeling Environment Or you may proceed immediately to the next tutorial Managing Models and More Managing Models and More This chapter contains a progressive tutorial designed to show you some more functions of the Visualizer including managing multiple models copying between model spaces measuring models and printing You also get additional practice at loading saving and sketching models This chapter is divided into three parts Before you begin provides some introductory and overview information Step by step tutorial gives you specific instructions to follow
131. O We use 0 5 and 15 5 rather than 1 and 15 so that divisions between colors occur between the atomic weights of atoms in our model In addition we use 15 5 rather than 16 5 because the PEN_COLORS color range contains 15 useable color entries as we can see by display ing the color range Check the Show Range check box A color range appears on the right side of the model window The first entry zero is invisible since it is black and so is the window back 30 Cerius Modeling Environment April 1999 What you can do with a model display ground Set the the Minimum and Maximum range color entry num bers in the Color Scheme section of the control panel to 1 and 15 respectively Select all atoms Then go to the Color Selected Objects control panel and choose Mass from the Color by a Property list All atoms except the oxygens are colored according to their atomic mass We can color the oxygens by treating masses above 15 5 as out liers In the Edit Color Mappings control panel click the Outliers pushbutton next to the Max entry box to access the Maximum Outlier Handling control panel Check the Pin to Maximum check box Oxygen is colored according to the maximum color entry number 15 Check the Use Pen check box and choose a color from the Use Pen popup Oxygen is colored with your chosen color You can experiment with some of the other controls in this cont
132. ODB are optional and can appear in any sequence When Cerius expects a token descriptor in an ODB and does not find one a default value is used for the associ ated attribute gt PLOT XY DATA name version name This is the character name by which the data set can be referenced Cerius Modeling Environment April 1999 429 D File Formats Descriptors 2D data set ODB Initiation record Descriptors version This optional integer can be used to distinguish different versions of data sets that share the same name When loaded the sequence of these numbers among the data sets is pre served Descriptors are any number of records each containing two blank delimited real numbers They define the x and y ordinates of each point in the data set gt PLOT 2D DATA name version name This is the character name by which the data set can be referenced version This optional integer can be used to distinguish different versions of data sets that share the same name When loaded the sequence of these numbers among the data sets is pre served SYSTEM POLAR CARTESIAN The coordinate system of the data set This must match the SYSTEM of any graph referencing the data set SYMMETRY NONE LATTICE XREFLECT YREFLECT XYRE FLECT QUADRANT LATTICE means regular unit cell repeats and is for Cartesian systems only XREFLECT YREFLECT and XYREFLECT are for Cartesian systems onl
133. OLSIONS 2 n Sos Gta eG ee ow aTa Gaye aT aes 220 Version S cise n a aa DEn AED var AE n at AE wet aderie AUS 221 Calculating close contacts 2 6 eee eee 222 Model surfaces 0 cece 223 Connolly surfaces 6 6 cece eae 223 Vector properties 6 ees 226 8 Viewing and Displaying Models 229 Moving models on the screen 0 0 0 c eee eee 230 Basic tasks and methods n nuanua annann nnn 231 Translating models 0 00 ana 232 Rotating models 66 c cece eee 233 Changing the view magnification 234 Setting position and orientation 236 Moving models relative to one another 237 Superimposing models 0 0 c eee eee ee 239 Storing and retrieving VieWS 6 66 0 scene 240 Animating models 0 0 00 c cece eee eee 241 Labeling and annotating models 045 242 Abel S ics sees endive iens es Bana aah ie Pan GE WY ate 243 INO LABEL capers bane Suelo aE es 243 NUMBERS isn tita Deere eee a oes ET 243 SYM INU Mere ofa tec om ea Acana a gia anhaa 243 ELEMENTS a csi fo Saree ahaa eee git tana a N 243 CHARGES os deno Teenaa Darks Giada eis Shar 243 FORMAL CHARGE 0 cece ee aes 243 OCCUPANCY siciaveanat raie Suid Bete oes 243 ISOTROPIC ent cme einen oes ea nie 243 FFEYT PE iatan ty EA tech a ea are eh a ea Bh 243 HYBRID i eaen at a alte arab adars Ara 243 NAME i sala Si i haoni at i a a ata a nen 243 MAS Siirry a E r ined E AEST YN 243 CHIRALIT
134. Other builders 0 ee 191 6 Managing Models and Sessions 195 Loading model structure files 00 0 c eee eee 196 Handling multiple models 0 0 00 c eee eee 199 Basic mode aana rini tasks aa naam han anaiai 200 Creating clearing and deleting model spaces 201 Specifying the current model 202 Selecting model spaces 1 06 0 eee eens 203 Controlling model visibility and the display mode203 Renaming models 6 6 0 0c eee eee eee 205 Sorting model table entries 00 205 Moving models between model spaces 206 Copying whole models from one model space to another 06 Mowing parts of models from one model space to another 20 Copying models to and from other applications 208 Saving model structure files 1 0 eee eee 209 Saving individual models 0000s aes 209 Saving all models 6 ccc cee eee 211 Working with Cerius sessions o n eas uae ase 211 Starting a NeW Session 6 sasur rnrn nnno 212 Saving the current session 0 0 0 e eee eee 212 Loading a previously saved session 213 vii Cerus Modeling Environment April 1999 Using saved sessions as preferences settings 214 7 Geometry Analysis 217 Measuring models 6660 c eee 218 DISTANCES cs iaa a iiaa a a Ha s fan irat alando tle a len aes ah iaai 219 PUGS isis Gratis teas DEAE aa aE E Ee SALON 219 Planes re opine ar hg a E ced aE S a 220 L
135. Some menu card entries provide direct access to control panels others whose labels end with an arrow give access to pullright menus which each give access to a control panel A Reset control shown in red letters appears on most cards and can be used to reset the controls for that module You can select a specific deck of cards from the deck selector popup by clicking and dragging Alternatively you can cycle backwards or forwards through available card decks by clicking the left or right directional buttons next to the deck selector popup Menu cards are grouped into decks of 1 5 cards which usually represent modules having related functionality To bring any card in the current deck to the front simply click the card s title You can customize the deck of cards menu by using controls in the Utilities pulldown menu on the main control panel s menu bar You can make new decks name them change the card order and so on For details see Customizing the Interface Cerius Modeling Environment April 1999 137 4 The Cerius Interface Contols and contol panels Definition Control panels are windows that contain functionally grouped Cerius controls Many different control types are available each designed to provide an intuitive method of invoking an action providing a value setting an option or selecting an item The con trol panel below illustrates many types of controls 138 Cerius Modeling Environment April
136. Some uses pencolors Structure displays in model window simple line graphs filled circ le plots colorwheel Masscloud plots Sorption module probe surfaces forfield calcula tions greyscale HRTEM simulations diffraction pattems graphs electrostatic Graphs difference colors spectrum Graphs color colors 270 Cerius Modeling Environment April 1999 Finding information Concepts Viewing color ranges Identifying critical and noncritical entries Customizing display colors This section includes information on Creating and editing a new color range Editing a color range To facilitate editing color ranges or constructing your own color ranges several concepts need to be defined Critical entries are points within a color range for which relative red green and blue color values are specifically defined and between which Cerius automatically interpolates colors Each color range must contain at least two critical entries defin ing the ends of the range for example only the two end values of the greyscale color range are defined A color range may contain more than two critical entries the two endpoints and one or more points in between as well as interpolated colors for example the electrostatic color wheel and spectrum color ranges have many critical entries A color range may be composed of only critical entries for example the pen colors color range Noncritical entries are
137. Values and mathematical expressions Table 19 Binary model operators in Cerius table expressions Operator Retums Description torsion number Torsion angle atoms referenced using a named quad Usage torsion col structure C1 C2 C3 C 4 torsionbyname number Torsion angle atoms referenced using a userassigned name Usa ge torsion col structure CA CB CC CD userdata text Retum the named userdata from the object if the field exists Amay based user data fields are not supported Usage userdata col structure Rotatable Torsions Additional information Please see the on screen help for details on the functioning of each control in the Tabulate Atom Properties control panel Manipulating text Unary text operators Unary text operators Table 20 take one argument that must eval uate to characters This argument either controls the operation of the function or is the text to be operated upon Table 20 Unary text operators in Cerius table expressions Operator Retums Description cdate text Retum time and date based on the input argu ment TODAY Today sdate NOW Today sdate and time YEAR Cunent year MONTH Curent month DAY Curent day DOW Cunent day of the week TIME Curent time ctext text Convert an entity to a text string reverse text Reverse the orderof charactersin a string strlen number Retum the length of a string tolower text Convert text to lowercase toupper text Con
138. Y os tise ied ssi eno tae ba oa 243 Default annotation 0 0 00 ccc eee 244 Custom annotations n sses cece 245 Model display style 0 eee 248 Atom and bond display styles 249 Bonds as sticks 2 eee ees 249 Cerius Modeling Environment April 1999 ix Bond order display 6 00 0c eee eens 250 Bonds as cylinders a na nsaan nannan 251 TONE ATOMS i Sra aan aurea aaa DE OAE a Bat 252 Atoms as balls 2 0 0 cece 252 Ball and stick models 00000 e eae 252 Cations as polyhedra 0 0 0 0 eee eae 253 Thermal ellipsoids 0 060 e eee eee 254 Structure traces kee 255 Cross sections of models 1 6 6 6 6 cece eee eee 256 Apparent depth effects 0 0 ccc eee eee 257 Depth cueing 0 6 cee ees 257 Projections ia wt A EE ia a Sete we oe 257 Resolution and graphical quality 005 258 Printing models and graphs 0 0 0 cece eee eee 259 9 Enhancing Model Display 263 Model display colors n sannan cece eee 264 Default element colors 06 6 cee eens 265 Coloring selected objects 0 c eee eee eee 265 Coloring atoms by properties 0 000 267 Background color in model window 268 Customizing display colors s a s sssaaa c eee eee eee 268 Drawing Colors 6 6 eee 269 Color ranges a iaiia E a eee 270 Creating and editing a new color range 272 Editing a color range 06 c eee ee eae 273 Property
139. a module double click the cell or the column or row heading Cerius Modeling Environment April 1999 349 11 Working with Tables Models in tables Cerius tables can store model information in table cells and can display this information in several formats Setting display formats You can also store atoms bonds and several other types of chem ical data in the columns and cells of Cerius tables Uses of model data in You can perform certain model specific operations on model col tables umns and can include model operators in mathematical expres sions Values and mathematical expressions in other columns that refer to a cell containing a model Finding information This section includes information on Copying models into columns Setting up calculations on models Saving tables containing models You should already How to access the Tables module is described under Accessing the know tools How to select a table for display and editing Specifying the current table and how to make sure control panels are connected to the desired table window Keeping track of the current table are dis cussed above How to select columns Selecting rows and columns and make a cell current Selecting a cell are described above Copying models into columns Tables generated and presented by other Cerius modules such as QSAR may contain models in columns You cannot copy models from the model window to a model data type
140. a 358 searches results 359 361 searches setting up 357 searches tests in 358 searching 354 357 selecting all cells 322 selecting items 322 sort criteria 362 sort order 362 sorting 361 stored values 321 structure diagrams 331 subsets 359 text 331 types of data 329 updating 349 values 334 viewing parts 359 TABLES amp GRAPHS card deck 292 313 TABLES card 313 Tables module 313 Tabulate Atom Properties control panel 351 352 Tcl scripting language 130 348 376 379 temperature factors anisotropic 187 254 command line entry 189 190 conventions 187 editing 189 formats 187 in Cerius2 187 isotropic 187 loading 190 mathematical forms 188 saving 190 210 specifying 188 Siete 427 theory 186 Cerius Modeling Environment April 1999 449 template tool 9 templates adding to a model 155 custom 155 loading 154 making your own 155 saving 156 specifying 154 use in building 154 155 Templates button 14 text messages 130 text window 128 382 thermal motion 254 Todino G 6 399 toggle definition 132 toolbar function 133 illustration 22 135 tools active 10 152 color coding 395 colors 394 dark purple 152 double clicking vs single clicking 150 topography 223 Torsion tool 220 torsions changing 173 measuring 174 220 352 trajectory 241 transition metals 182 Translate Atoms control panel 175 176 177 transparency display style 278 tutorials boxes 6 introduction to Cerius2 5 introductory 6 layout printed
141. a Dynamics Trajectory file with an update every 100 steps Trajectory Update Frequency This means that during the 2000 step simulation 20 trajectory frames will be saved for later analysis Type in glucose_water as the Filename Prefix Return to the Dynamics Simulation menu and select the Run Dynamics button As the simulation continues the structure on the graphics screen is updated every 25 steps Notice the changing H bond pattern The graphs show that the temperature of the simulation fluctuates around 124 Cerius Modeling Environment April 1999 What to do next the requested 300K What to do next This simple simulation might be useful to provide insight into hydrogen bonding patterns and dynamic behavior To obtain a more quantitative measure of hydrogen bonding between water and beta B glucose the calculation could be repeated with a larger number of water molecules using periodic boundary conditions The resulting trajectory file could be analyzed to predict the pair correlation func tion between the hydroxyl groups on the glucose and the water Or ae aL 10 W g oh r 0 00 0 00 separation The area under the h bond peaks is proportional to the number of hydrogen bonds in the system and can be compared to results for other systems for example to other carbohydrates It is known that monosaccharides in water undergo structural isomerization Processes that involve bond break
142. a a AS 419 CAMBRIDGE read only 2 cece 421 CIF read only a a a EE A LET 421 CSSR a a a a E lar E a E ee a e N 423 ICSD read only 2 eee 424 MACCS Molfile 0 0 ce ee 424 M l EN Aa oh death Sete anata 2k Sa Rants eet Sante eat Atha 425 MOPA Cons visas oa Gite aed woe CRANE ety Gt sec ee 425 PID Bs aise ocean Se ae ahaa Sea sea aha ee aa 426 SHE DEX potai a a EE E A mn dears Sea 427 Loading and saving temperature factors in structure files 427 Gira ice Bou aie win bk hs ares ges ee a ak we ae 428 Heade r record rincon erasa i oa ee a 428 COMMONS we ie ih eee Hone ek ae Se Bee el N 429 Object definition blocks 1 0 eee eee 429 X Y data set ODB 00 eens 429 2D dataset ODB 0 0 cece eee eee 430 X Y Pans attribute ODB 04 431 2D plotting attribute ODB 4 431 Cerius Modeling Environment April 1999 xiii 2D graph ODB eiee cece 432 Gallery ODB oirne asia munaan alsa s apenteie aera aa 433 Termination record 0 0 0 cece ees 433 Xy and con files nanna nannaa 434 File documentation at our website xiv Cerius Modeling Environment April 1999 Important Using this guide How To Use This Guide If this is the first time you ve used Cerius please skip this chapter for now and go directly to Introducing Cerius2 This documentation set Cerius Modeling Environment is a com plete guide to the Cerius modeling environment
143. access the Disorder control panel You can use this control panel to Apply the disordering to the whole model or to selected atoms Specify the displacement distance in angstroms for each atom that is to be moved in a random direction Please see the on screen help for details on the functioning of each control in the Disorder control panel Temperature factors Finding information Related information Temperature factors and atomic vibrations If you need to know only how to work with temperature factors within the Cerius interface you may skip this theory section and go directly to Specifying temperature factors Editing temperature factors Loading and saving temperature factors Representing the thermal motions of atoms graphically is dis cussed under Thermal ellipsoids Atomic vibrations are described in the lowest order by their tem perature factors If the deviation of an atom from its equilibrium position is r x y z the vibration is characterized by the matrix x xy x2 H yx y2 y2 Eq zx zy z2 Where xy represents the average over many vibrations 186 Cerius Modeling Environment April 1999 Anisotropic and isotropic temperature factors Effects of vibration on X ray scattering Conventions Cartesian and crystal coordinate systems Temperature factors in Cerius Advanced building and editing H is symmetric and contains six independent quantities th
144. access the Process Management control panel To specify what process you want to start or stop select its name from the Application list box in the Process Management control panel The name of the relevant process appears in the Process list box If you are unsure of the application name assigned to a module go to the module open any of its control panels and use the right mouse button to request help The first line of the help window that appears contains the application name The names of machines on your network appear in the Host list box Select the one that you want to send the process to The machine you are running Cerius on is called localhost If a machine s name is not on that list but you know it is accessible from your machine you can enter its name in the Remote Host entry box If you need a password in order to use the specified machine enter it in the Password entry box 386 Cerius Modeling Environment April 1999 Tip Starting an external pro cess Ending an external pro cess Additional information Related information Running application modules extemally To determine whether you must enter a password enter the command rsh hostname in a separate shell window If you are not prompted for a password to log on to the specified remote host a password is not required here To specify your working directory on the specified host if it does not appear automatically enter the name of
145. aces 330 default cell format 321 default numeric data type 321 deleting columns or rows 324 325 448 Cerius Modeling Environment April 1999 derived cells 334 derived columns 334 derived values 334 display format 330 displaying parts 359 editing 321 empty 317 entering changes 321 entering mathematical expressions 335 entering values 321 exporting 365 finding information 357 floating point real numbers 330 format 330 from an ASCII file 319 graphing 363 graphs updating 365 groups 353 groups copying 354 groups creating 354 groups deleting 356 groups editing 355 groups selecting 356 groups viewing 360 headings 331 332 implicit selection 322 importing data 319 index 334 inserting columns or rows 325 labels 331 334 lines between cells 333 loading from file 318 mathematical expressions 333 model identification numbers 331 models 331 350 models copying 350 models sorting 362 moving columns or rows 323 moving values 322 named groups 353 new 317 nonscrolling columns or rows 331 332 opening 318 pasting values 323 plotting 363 previously saved version 318 real numbers 330 rearranging 322 recalculating 349 352 recovering from errors 318 removing 327 resetting the view 360 361 rounding 321 row height 332 row labels 331 row numbers 331 rows selecting 322 saving 326 365 saving with models 352 scientific notation 330 search and replace 359 searches comparison criteri
146. ain Visualizer control panel to access the Edit Color Ranges control panel Alternatively if you have the Color Selected Objects control panel open Accessing the tools you can click its Color Ranges pushbutton to access the Color by Range control panel and then click the Edit Ranges pushbutton to access the Edit Color Ranges control panel Choose the name of the range you want to edit from the Color Range popup The current values for the number of colors in the range and the numbers of the critical entries appear The color def initions appear in the sliders when you choose a critical entry from the Edit Critical Color Entries list If you saved the custom color range during some earlier Cerius session Saving a color range you have to load that session to access that color range see Loading a previously saved session Edit the color entries by the same procedure as used in creating a color range Creating and editing a new color range Cerius Modeling Environment April 1999 273 9 Enhancing Model Display Additional information You can also use the Edit Color Ranges control panel to delete or rename an entire color range or to remove a selected critical color You should not delete either of the end colors Please see the on screen help for details on the functioning of each control in the Edit Color Ranges control panel Property c olor mapping Uses of color maps Finding information Related inf
147. alculation file and other operations are applied To specify that a certain model be current click the current model indicator diamond shaped button to the left of its name in the model table The current model is identified by a red diamond all other diamonds are greyed out Alternatively you can press lt Ctrl gt on the keyboard and click any atom in the desired model with the left mouse button The current model is always visible in the model window as the only model in the model window in the lower left corner of a multi paned model window displaying many models in grid or border mode Controlling model visibility and the display mode or as one of the models displayed in overlay mode Controlling model visibility and the display mode A tutorial example of handling multiple models is found under Managing multiple models 202 Cerius Modeling Environment April 1999 Selecting model spaces Selecting models Handling multiple models You can select one or more model spacess On which to perform model management operations To be used by various application modules To select model spaces click the model ID number s in the model table using the left mouse button A single click selects only one model You can select more than one model or change what is selected To select several models click the first model ID number and then drag to select several contiguous models and or lt Shift gt click to sele
148. all selected atoms simultaneously You can also Select atom s and then select the Edit Delete menu item or the Edit Cut menu item Select atom s and then press lt Ctrl gt lt Delete gt simultaneously while the cursor is in the model window Deleting only bonds To delete a bond between two atoms without deleting any atoms use the Delete Bond tool You can Select the Delete Bond tool and then pick the atoms whose bond you want to delete or Select the desired bonded atom pairs s and then double click the Delete Bond tool to delete all bonds between selected atoms simultaneously You can also 170 Cerius Modeling Environment April 1999 Basic editing Delete bonds between all atoms or between selected atoms with the Delete bonds action button in the Edit Connectivity and Bonding control panel Access this control panel by selecting the Build Edit Bonds menu item Delete hydrogen bonds Hydrogen bonds between all or selected atoms with the Delete H bonds button in the Edit Hydrogen Bonding control panel Access this control panel by selecting the Build Edit H Bonds menu item Duplicating parts of a model To make copies of all or part of a model select the desired atom and then select the Edit Duplicate menu item or press lt Alt gt 1 on the keyboard This performs a copy and paste operation produc ing an offset copy of the selected atoms You can also copy or move parts of models
149. and script file Managing licenses nnana nannan nrnna Running application modules externally 14 Customizing the Interface Interface configuration 06 66 cee eee Deck of cards menu configuration 4 Control panel management 00000 e eae Interface look and feel 0 ccc aaa Interface colors 0 ee es Miscellaneous environment customizations xii Cerius Modeling Environment April 1999 A References 399 B Definitions 401 Models fragments and templates 0000005 401 Glossary cs s 0 tas eis a aes es ea eee ais 402 C Mouse and Keyboard Actions 407 Mouse actions 0 0 cece ee eee tenes 407 Control panels sipe aiii Ee Kaana eee 408 Any CONTO eita Doe pe E eens 408 File browser 2 0 0 0 cece eee eee eee 408 Model table 0 cece eee 409 Graph window 0 000 cc eee eee eee eee 409 Model window 000 cece ee ee eee 410 Tabl wWitdOw sron hea tae elie a he eae e 411 Cursor over individual cell 0055 411 Cursor over row or column heading 411 Keyboard shortcuts 0 eee 411 Graph window seasea ccc cece eee eee 412 Model window 0000 c cece eee eee eee 412 Table window wore aoste n ccc ce eee ee eee 412 D File Formats 415 Structure files cad irupo Pd ek we Pa ech ahs eae 416 SMe cafe a AE E E UUENA 416 MOF ai a E A ena i ch adh SRE a AA 20h a TRA aah SG a a 418 POE n r Aa ea A NEE wer A Aa
150. and which is the mov able model by selecting them from the pulldowns or typing their model numbers or names in the text entry boxes The number of atoms specified in the reference model must be the same as the number in the moving model If you want to take all atoms into account during the fitting the models must have the same number of atoms and they must be numbered identically you can label a model according to atom numbers see Labels If this is true you don t need to select atoms in order to specify them Cerius Modeling Environment April 1999 239 8 Viewing and Displaying Models Performing the superim position Additional information Related information If you want or need to select the atoms to be matched select them in the same order in both models If atoms in the two models are numbered identically and you want to superimpose identically numbered atoms you need select atoms only in one model You can mass weight the calculation for example if the positions of hydrogens are less important by setting the atom weighting popup to MASS Be sure that all desired atoms are still selected then click the MATCH pushbutton to superimpose the models and report the rms fit in the text window Please see the on screen help for details on the functioning of each control in the Match Atoms control panel Selecting atoms in more than one model is discussed in Selecting atoms in several models The Cerius Align
151. anel All menu cards that are available at your site are listed in the Licensed Cards list box Select one or more of the menu cards by clicking its name in this list Selected card names become high lighted Deselect a card by clicking a highlighted name again To create anew card deck click the ADD NEW DECK pushbutton in the Customize Menu Deck control panel 390 Cerius Modeling Environment April 1999 Editing deck contents Saving the new deck con figuration How it works Interface configuration To rename any card deck choose the deck from the deck selector popup above the list box toward the right side of the Customize Menu Deck control panel Enter the new name in the Rename Deck entry box To delete a selected deck click the DELETE DECK pushbutton The cards that were in that deck are still available in the Licensed Cards list box for inclusion in other decks if desired To change what cards are in a deck or the order in which they appear choose the deck you want to edit from the deck selector popup above the list box toward the right side of the Customize Menu Deck control panel The menu cards currently included in this deck are shown in the list box below its name in the virtual top to bottom order in which they appear in the deck when it is first opened in the Visualizer main control panel To add selected cards from the Licensed Cards list box to the cur rent menu deck up to a maximum of fiv
152. anels are given throughout this guide Tip Closing control panels Cascading contro panels Stowing all Cerius win dows to an icon Additional information Often a control panel can be accessed in several different ways Since Cerius is amodal it makes no difference how you access a particular control panel or whether you close and reopen it or just leave a frequently used panel open on the computer screen To close a control panel click the close button Pi in the upper right corner of the control panel s border To close all open control panels click the clear panels tool Bl on the toolbar of the Visualizer main panel To group all open control panels into an orderly cascade click the cascade panels tool eB on the toolbar of the Visualizer main panel To stow all open Cerius windows to a single icon on your desk top click the stow button on the upper window border of the main control panel To open the windows again simply click the icon on your desktop More advanced management of control panels including custom ization so that certain control panels are opened whenever you start Cerius is discussed under Control panel management Cerius Modeling Environment April1999 141 4 The Cerius Interface Information sources On screen help Example While using Cerius you can obtain information about every con trol and menu item by using the on screen help facility To obtain a help w
153. are the main control panel which contains the Visualizer controls the model window in which models are dis played and the text window which is used to display text mes sages Their initial screen orientation is shown below except that the large square window should be black on your screen 128 Cerius Modeling Environment April 1999 Initial layout of the Cerius screen Main contol panel Model window Text window Main contol panel The main control panel contains the Visualizer controls and is therefore your primary point of interaction with Cerius All con trol panels are obtained directly or indirectly from the main control panel Unlike ordinary control panels however the main control panel should not be resized You may stow iconify the main con trol panel by clicking the stow button on the window border This stows all open Cerius windows to a single icon on your desktop If you try to close it a warning message appears asking you to confirm that you want to quit the Cerius session Cerius Modeling Environment April1999 129 4 The Cerius Interface For details on using the main control panel please see Using the main control panel Model window Mouse and keyboard shortcuts Cerius provides real time 3D graphic display of models in the model window The models displayed the style of display model orientation and so on are determined primarily by Visualizer con trols accessible
154. artial atomic charge of a named atom Usage charge col structure C1 Partial atomic charge of an atom referenced using a user assigned name Usage charge col structure CA Interatomic distance atoms referenced using a named pain Usage distance col structure C1 C 2 Interatomic distance atoms referenced using a user assigned name Usage distance col structure CA CB Count the number of occurencesofa specified element Usage ecount col structure C Perform an exact search foran object and count the number of occurences found Hydrogensare not ignored Usage exact col structure cell frag_tbl CO Calculate various steric properties of a molecule No coordinate transformationsare made aspartof thiscalculation Thus the result of thiscalculation changesasthe molecule isreoriented Properties are RX Range of x coordinate values RY Range of y coordinate values RZ Range of zcoordinate values MINX Smallest x coordinate value MINY Smallest y coordinate value MINZ Smallest z coordinate value MAXX Largest x coordinate value MAXY Largest y coordinate value MAXZ Largest z coordinate value VOLUME Volume of the box in which the molecule is contained Usage smol col structure RX Perform a substructure search foran object and count the number of occurences found Hydrogens are ignored Usage sss col structure cell frag_tbl CO 346 Cerius Modeling Environment April 1999
155. at is which color repre sents a high value and which low Whether the color scale is applied in a linear or log way The number of contours used in contour style 2D graphs fewer contours means faster redrawing when you make changes 304 Cerius Modeling Environment April 1999 Additional information Managing graphs How smooth is the color shading for continuous style 2D graphs The range of values that are mapped to colors The exposure brightness and contrast of the displayed colors Please see the on screen help for details on the functioning of each control in the Plotting Attributes control panel Managing graphs Why read this section Finding information Related information You should already know You may be running an application that produces many graphs However you can for example control how new graphs are added to the graphing system and remove graphs from the gallery manager This section includes information on Controlling default display format Preventing replacement of old graphs Removing graphs and data from a Cerius2 session Saving graphs Controlling which one s of several plots which are held in com puter memory during a Cerius session are displayed in the Cerius2 Graphs window is discussed under Selecting and displaying graphs Saving preferences is discussed under Using saved sessions as pref erences settings How to access the Graphs module is descri
156. at is discussed in Saving a table However if you want to save only part of a table in MSI format you need to use the procedure described here How to access the Tables module is described under Accessing the tools How to select a table for display and editing Specifying the current table and how to make sure control panels are connected to the desired table window Keeping track of the current table are dis cussed above Selecting columns and rows is discussed under Selecting rows and columns To export table contents you need to access the Export Table con trol panel Click the EXPORT tool in the current table tool bar or Select the File Export menu item from the TABLES card Cerius Modeling Environment April 1999 365 11 Working with Tables Exporting table informa tion Additional information To select the file format in which to save the current table set the Format popup as desired To save the entire table select the Entire Table control Columns containing model data Models in tables cannot be saved in any for mat other than MSI However you may save other columns in your table in any available format by selecting only part of the table To save selected row s and or column s select the Selection con trol To save a group if present in the table see Grouping table infor mation select the Group control and choose a group name from the associated popup To set any additional options
157. at the direction be calcu lated as the best fit vector through the currently selected atoms not necessarily the same atoms that you select to move If symmetry constraints do not allow the requested translation the closest permitted translation is made instead Cerius Modeling Environment April 1999 175 5 Building Models Additional information Rotating atoms manually Rotating atoms precisely Additional information Please see the on screen help for details on the functioning of each control in the Translate Atoms control panel You can rotate selected atoms around all three axes by using the mouse to control the cursor in the model window To rotate selected atoms Around the x axis Drag the cursor vertically while holding down lt Ctrl gt and the right mouse button Around the y axis Drag the cursor horizontally while holding down lt Ctrl gt and the right mouse button Around the z axis Place the cursor close to an edge of the model window and drag it parallel to that window edge while holding down lt Ctrl gt and the right mouse button More than one atom should be selected Symmetry considerations in periodic systems may not allow certain rotations Tables of mouse button and keyboard combinations are included in Mouse and Keyboard Actions To rotate selected atoms by a precise angle around a specified rota tion axis and center select the Move Atoms Rotate menu item to access the Rotate
158. atch up the atom serial numbers in the text window with the atoms in the model window Cerius Modeling Environment April1999 87 3 Tutorials 3 Optional step Load the model Cerius2 Models molecular crystals pig ments indigo_1 msi This is a crystal structure of indigo Perform the same measurements on this model as you made on the indigo that you sketched Compare the results Because the model that you made was only crudely minimized by the Clean tool and not affected by crystal packing constraints you ll notice significant differences between the two models Finish by choosing the Delete Measurements button This removes all the measure lines and values from the models E Generating hard copy In the following steps you output the contents of the model win dow to a PostScript file and then print a view of the trinitrophenol model in ball display Note This exercise assumes that you are able to print grayscale PostScript files from your workstation Make trinitrophenol the current model and the only model visible Set the display style to Ball 88 Cerius Modeling Environment April 1999 Managing Modelsand More If necessary rotate scale or translate the model in order to get a pleas ing view of it in the model window Open the Print control panel by selecting Print from the File pulldown menu Choose the Page Setup button to open the Page Setup
159. ated subset This section includes information on Viewing named groups Viewing search results Cerius Modeling Environment April 1999 359 11 Working with Tables You should already know How to access the Tables module is described under Accessing the tools How to select a table for display and editing Specifying the current table and how to make sure control panels are connected to the desired table window Keeping track of the current table are dis cussed above Viewing named groups Accessing the tools Viewing named groups Viewing the whole table Related information Additional information To view only a named group you need to access the Table Groups control panel Click the GROUPS tool in the table manager tool bar or Select the Data Groups menu item from the TABLES card To view only an existing group select the name of that group by clicking its name in the Groups In Table list box in the Table Groups control panel Click the VIEW pushbutton To view the entire table do one of thee Click the RESTORE VIEW pushbutton in the Table Groups control panel Click the RESTORE VIEW tool in the table manager tool bar Select the Data Restore View menu item from the TABLES card Creation of named groups is discussed under Grouping table infor mation If you just want to highlight the desired named group without hiding columns or rows that are not in the group please see S
160. ately like this 18 Cerius Modeling Environment April 1999 Building a model caffeine we Still bad but you re getting there 9 Correcting the hydrogens In the Sketcher control panel click the H ADJUST button Now except perhaps for some strange bond lengths or angles your caffeine model is nearly finished 10 Cleaning up the conformation Still in the Sketcher control panel click and hold the CLEAN button until the model stops moving Now your model should be finished and look like Cerius Modeling Environment April1999 19 2 Introducing C erius Note In fact your model may not really be finished The algorithm that the CLEAN button uses to improve the structure was written more for robustness and speed than for high accuracy Therefore if you want a model that is chemically even more realistic and depending on the structural accuracy needed for your computational experiments you would generally want to further optimize the structure For this you would use one of the forcefield or quantum based products such as CDiscover or ADF all of which have their own documentation Click the selection tool the arrow icon in the upper left of the Sketcher control panel to return the cursor to its selection function Alternatively you can simply close the Sketcher control panel since you don t need it for a while The cursor should now be a plain arrow w
161. atoms you can specify a distance in terms of number of bonds within which atoms should be excluded For example a bond separation of 1 means to exclude only directly bonded atoms from the search Choose BONDED and enter the Separation in number of bonds For example figure below if the bond separation is 1 the dis tances between directly bonded atoms 1 2 and 2 3 are ignored If the bond separation is 2 the distance between atoms 1 and 3 is also ignored a ee iil 222 Cerius Modeling Environment April 1999 Calculating close con tacts Display of close contacts Additional information Model surfaces Groups Defining and selecting groups are defined with the Groups control panel which is accessed by clicking the Define Groups pushbutton on the Close Contacts control panel or by selecting Edit Groups from the menu bar A fragment includes all members of a bonded set of atoms You would for example set the exclusion to FRAGMENT if you were examining the fit of a small molecule to a receptor or surface in the same model and wanted to ignore any close contacts within a frag ment However if the small molecule and receptor were present as different models you would set the exclusion to MODEL Set the selection criteria and then click the CALCULATE close contacts action button to calculate and display close contacts Once calculated close contacts are continuously updated when fragments are moved rotated c
162. ault position and direction and can be returned to the default position or direction by clicking the appropriate reset action button To change the position through which the slice plane slices the grid use the Position arrows to move the slice up or down the per pendicular to the slice plane The numbers show the position that the slice plane passes through They change as you click the arrows or you can edit them directly To change the direction of the line perpendicular to the slice plane up and down which the plane can be moved edit the numbers in the Direction entry box Clicking the Preferences pushbutton gives you access to the Slice Preferences control panel which contains additional controls that affect slices To create a 2D contour graph corresponding to a selected slice plane click the Create Slice Plot in Graph Window action button in the Slices control panel Please see the on screen help for details on the functioning of each control Cerius Modeling Environment April 1999 373 12 Working with Isosurfaces 374 Cerius Modeling Environment April 1999 This section explains Scripts and Licensing All Cerius applications including the Visualizer are command driven The graphical interface takes your input mouse clicks and drags etc continuously translates it into commands records the commands into logs and passes the commands to the programs themselves Although many users general
163. aults 46 Cerius Modeling Environment April 1999 Summa ry Some of what you ve lea med 40 Finding additional information Detailed information on all the functions of the Visualizer are found in the other sections of this documentation set Tables of the mouse and keyboard functions can be found under Mouse and Keyboard Actions Detailed information about modules other than the Visualizer are found in the documentation for the applications to which those modules belong 2 41 Quitting your Cerius session Select the File Exit menu option Click Exit in the confirma tion window that appears Summary Some of what you ve leamed Sections of this book where you can find additional information are listed in bold type in this list 1 Using and managing menus windows and other controls in the Cerius interface e g Locating the basic building tool Clean ing up your screen see also The Cerius2 Interface 0 Building models see Building a model caffeine Building another model ferrocene see also Building Models QO Sketching with templates and ligands see Sketching the ring sys tem of caffeine Here s another way of adding a methyl group Adding the ligands see also Adding templates groups of atoms 0 Changing atom elements and bond types see The Edit Element tool looks like Correcting the bond order see also Changing atoms and their bonding types LI Using the periodic tab
164. ay the Graph Scaling control panel For 2D Cartesian graphs you can also set the range values relative to the width of the data set For x y graphs you can also choose among several options for automatic axis scaling by choosing from the Axis Scaling popup in the Graph Scaling control panel To force the axes in a 2D Cartesian graph to be drawn perpendicu larly check the Force Rectangular Axes check box in the Graph Scaling control panel For example check this box when viewing HRTEM output for nonorthogonal periodic cells to view the graph as a rectangle rather than a parallelogram To set the minimum and maximum displayed angles in 2D polar graphs use the Min Angle and Max Angle entry boxes in the Graph Scaling control panel The angles are defined clockwise in degrees from north up To set the displayed radius in 2D polar graphs use the Max Radius entry box in the Graph Scaling control panel To shift a curve or other representation of a data set up or down the y axis of an x y graph enter a value in the Y Offset entry box of the Plotting Attributes control panel This does not change the actual data points X y graphs can be scrolled along either axis To scroll the graph along the x or y axis use the arrow tools in the Scroll controls of the Graph Scaling control panel To return the view to its original position that is centered on the same area as before you began scrolling click the reset button in the ce
165. bed under Accessing the tools Contolling default display format When a graph is created by a Cerius application module the best graph axes annotations and plot attributes are set auto matically When a graph is loaded from file the format that was Cerius Modeling Environment April 1999 305 10 Working with Graphs Controlling formats in gen erated graphs and in graphs loaded from files Accessing the tools Resetting the default graph format saved with the file is used However you can set your own prefer ences For example in doing a series of Rietveld refinements you may be most interested in a particular data range After the graph from the first refinement appears you can zoom in on the desired data range and then set these graph axes as your preferences When graphs that are output from subsequent refinement are sent to the graph window the graph axes remain in your region of interest and do not revert to showing the entire data set By default when a graph file is loaded it uses the same axis scales types of annotations and other settings that were in effect when the file was saved However you can override some of these set tings before loading the graph file Select the Gallery Expert Functions menu item from the GRAPHS card to access the Graphs Expert Functions control panel Alternatively click the Expert Functions pushbutton in the Gallery Manager control panel to acces
166. ber atom label residue A3 1X A1 1X A5 name chain designator must be in uppercase orblank res 3F10 5 1X A5 13 idue number x y z coordinates in A atom type max no 12 1X F8 5 of covalent bonds no lone pairs atomic charge Note Only atom number label HX TX label monomerheads and tails coordinates types and chargesar relevant in Cerius The other variables are XXxGraf entities 13 FORMAT FORMAT CONECT record format specification if not present the CONECT CONECT default format isused FORMATCONECT format spec ifica 1X A tion for CONECTrecords 14 CONECT CONECT 1216 Connectivity list CONECT number of central atom atom numbers of atoms bonded to central atom 420 Cerius Modeling Environment April 1999 Struc ture files Record Format Storage 15 ORDER ORDER 1X 12I6 Bond order records ORDER number of central atom bond orders foratoms bonded to central atoms 0 1 single 2 double 3 triple bond The atom numbers in CONECTrecords represent the atom numbers of the equivalent unit cell atoms The following three recordsspecify whether the centralatom isbonded to an atom in the same cellora neighboring cell These record classesare present only in periodic files where there are one or more connections to a neighboring cell 16 DISPX DISPX 1X 12I6 X cell displacement record DISPX number of central atom xdifferencesin cellsofthe two connected atoms Valuesc
167. c IRIS IRIX and Silicon Graphics are trademarks of Silicon Graphics Inc AIX Risc System 6000 and IBM are registered trademarks of International Business Machines Inc UNIX is a registered trademark licensed exclusively by X Open Company Ltd PostScript is a trade mark of Adobe Systems Inc The X Window system is a trademark of the Massachusetts Institute of Technology NSF is a trademark of Sun Microsystems Inc FLEXIm is a trademark of Highland Software Inc Permission to Reprint Acknowledgments and References Molecular Simulations usually grants permission to republish or reprint material copy righted by Molecular Simulations provided that requests are first received in writing and that the required copyright credit line is used For information published in documentation the format is Reprinted with permission from Document name Month Year Molecular Simu lations Inc San Diego For example Reprinted with permission from Cerius Modeling Environment April 1999 Molecular Simulations Inc San Diego Requests should be submitted to MSI Scientific Support either through electronic mail to support msi com or in writing to U S version of Copyright Pages MSI Scientific Support and Customer Service 9685 Scranton Road San Diego CA 92121 3752 To print photographs or files of computational results figures and or data obtained using Molecular Simulations software acknowledge the source in the format Co
168. c click or click and drag It will be clear from the context Pick click an item usually an atom in the model window Check and uncheck click a check box so that it contains or does not contain respectively a checkmark Toggle click an on off control to change its state from on to off or vice versa Using the main contol panel The main control panel controls the Cerius e Visualizer Function alities are collected into related groups of controls 132 Ceru Modeling Environment April 1999 Menu bar Toolbar Model manager Deck of cards menu Parts of the main control panel Using the main control panel SURFACE BUILDER CRYSTAL BUILDER The menu bar contains pulldown menus that provide access to all Visualizer tools For descriptions of the menu bar entries see The menu bar The toolbar provides a set of frequently used Visualizer tools some of which are duplicated in control panels relating to model view ing and selection For full details see The toolbar The model manager enables you to control the selection editing and saving of models in the Cerius modeling environment The model manager is described fully under Handling multiple models Application modules are represented by menu cards grouped into card decks in the deck of cards menu For more information see Deck of cards menu Window manager controls located in the window border allow you to stow all open Cerius
169. cal interface for use in future Cerius sessions click the SAVE CONFIGURA TION pushbutton in the Customize GUI colors control panel When you click the SAVE CONFIGURATION pushbutton the current interface colors are saved to a file named gui_colors in an MSIguirc subdirectory in your home directory This file is auto matically read whenever you start Cerius If you create separate directories and copy the MSIguirc subdi rectory and its contents to the new directory for other purposes How it works How it works the copied gui_colors file should not be removed from this new directory Although you would proba bly not want to change the gui_colors file for different projects Cerius does not look for another MSIguirc subdirectory in your home directory if it finds an MSIguirc subdirectory in the direc tory in which you start it Please see the on screen help for details on the functioning of each control in the Customize GUI Colors control panel Cerius Modeling Environment April 1999 395 14 Customizing the Interface Misc ellaneous environment customizations Related information Accessing the tools Cerius as a desktop icon Starting with no banner Running in OpenGL mode See Interface configuration for information on changing the content of deck of card menus Running Cerius on one machine while displaying and interacting with its interface on another is discussed in the Cerius Installation a
170. cally appears in a separate Cerius2 Graphs window sometimes called a gallery You may want to change such things as How many graphs are currently displayed in the window The range of data points that are visible The text that accompanies a graph This section includes information on Selecting and displaying graphs Selecting which data sets to display and edit Labeling and annotating graphs Cerius Modeling Environment April 1999 297 10 Working with Graphs Related information You should already know Changing graph axes and scale Changing plotting style and color How to print the contents of the Cerius2 Graphs window is explained under Printing models and graphs How to access the Graphs module is described under Accessing the tools How to load graphs from files is described under Loading graphs Selecting and displaying graphs Accessing the tools Selecting graphs to dis play Accommodating graphs within the graph window Tip To display or edit graphs you need to select them Select the Gallery Manager menu item from the GRAPHS card to access the Gallery Manager control panel The graph window is also referred to as the gallery To display or hide particular graphs check or uncheck the appro priate check boxes in the Display column to the left of the list of graph names in the Gallery Manager control panel For changes in the graphs displayed to occur immediately make sure the A
171. ces must be enclosed in quotes Columns in Cerius tables may contain chemical models Models in tables and calculations may be performed using these models Unary model operators Table 18 take one argument which must evaluate to a cell of type molecular The operators return null if anything else is specified Examples of unary model operators are mw col Structure atoms col 1 bonds col 1 344 Cerius Modeling Environment April 1999 Values and mathematical expressions Table 18 Unary model operators in Cerius table expressions Operator Retums atoms number bonds number idtomol chemical data inttomol chemical data inttooid chemical data isvisible number makecurrent 0 zero mf text mw number numchildren number thename text Binary model operators Tip Description Number of atoms Number of bonds Convert a model ID number assigned in the model table into a model Convert an integer into a Ceru model if that integer referencesan entire model Convert an integer into a Cerius model component forexample an atom a bond oran entire model Retum 1 if the model is visible and 0 zero if the model is invisible Make the referenced model the current model Molecular formula Molecular weight The numberof dependent objects contained in the parent object For a model this includes the total numberof atomsand bonds along with any other objects included in the model
172. ch with tool In other words this control BA sxetch with ES Click Fe in the Periodic Table window The Sketch with entry box is filled in with Fe Actually you could have just entered Fe in the Sketch with entry box by typing but we wanted to show you the periodic table Click once somewhere near the center of the model window The single Fe atom is represented as a cross If you prefer the Fe to be represented as a ball select the View Dis play Attributes menu item Then in the Display Attributes con trol panel click the Preferences button In the Style Preferences control panel set Lone Atom Style to BALL Cerius Modeling Environment April1999 33 2 Introducing Cerius 27 Adding the ligands Click the Templates button in the Sketcher control panel In the Sketcher Template control panel double click ligands and then double click pentadienyl You may have to move up out of the organic directory if you haven t restarted Cerius since the beginning of this tutorial The template tool is now selected and allows you to add pentadienyl ligands to the iron Click the Fe atom This adds one ligand Click the Fe atom again Select the selection tool in the Sketcher control panel and move the model so that the rings appear to be nearly superim posed You ll notice that the ferrocene model is not symmetrical and that pre
173. cher menu item from the Visualizer s main control panel This causes the Sketcher control panel to appear This control panel provides a range of tools for mouse controlled sketching editing and refine ment of model structures Selection tool Sketc h with popup for selecting the f elementtype i Hieman CE Periodic table tools for Sketch with and Edit Hybrid Edit Hement tools respectively Edit Bond since Edit Formal as Charge E varoen PRBS Draw with Hydrogens Template tool How it works Clicking any of the icon tools on the Sketcher control panel alters the function of the left mouse button Selection mode when the Cerus Modeling Environment Apnrl 1999 149 5 Building Models Recovering from mistakes Help Examples selection tool the arrow in the upper left of the Sketcher control panel is highlighted is the default for cursor behavior Clicking other icon type tools enables you to use the cursor for example to place atoms manipulate angles or change an atom s element type Many of the functions can be performed on several atoms simulta neously This is done by first selecting Selecting atoms and groups of atoms the atoms then double clicking the appropriate tool If the tool is already active only one click is needed to perform the action In some Sketcher modes a property of the structure can be changed by moving the mouse in the model window Generally dragging left to right or bo
174. cise Cerius Modeling Environment April1999 49 3 Tutorials Before you begin To complete this tutorial you need a licensed copy of Cerius and a directory into which you can save the files you create during the tutorial In this tutorial you familiarize yourself with the look and feel of the Cerius GUI and Visualizer You use the Cerius menu bar File Edit Build etc and the tool bar immediately below it You learn how to load a model and then practice viewing displaying and selecting it The tutorial concludes with a brief exercise about control panels Summary of tutorial The tutorial is divided into four short exercises A Loading and displaying a molecular model B Viewing and labeling a model C Selecting atoms D Manipulating control panels Step by step tutorial This section takes you through a series of short progressive exercises designed to familiarize you with some basics of the Cerius Visual izer A Loading and displaying a molecular model In the following steps you load an msi format structure file of trim ethylbenzene and display it in both Stick and Ball styles 1 Start Cerius and load the model If Cerius isn t already open type gt cerius2 in a UNIX shell to run the program 50 Cerius Modeling Environment April 1999 Basic GUI Functions The program takes a few seconds to initialize a welcome screen appears briefly and then the Cerius GUI appear
175. ckground information Step by step tutorial gives you specific instructions to follow Review summarizes the exercise by giving a checklist of the skills you ve learned 62 Cerius Modeling Environment April 1999 Using the 3D Sketcher Before you begin Note To complete this tutorial you will need a licensed copy of Cerius and a directory into which you can save the files that you create dur ing the tutorial Before you begin the tutorial on page 50 you should be familiar with the contents of the section Basic GUI Functions If you have not read this section you should ensure that you know how to do the review items listed in the Review on page 61 before beginning this tutorial In Basic GUI Functions you loaded a model from file into the model window The purpose of this tutorial chapter is to show you how you can build your own models using the 3D molecular Sketcher The Sketcher is the principal building tool of the Cerius Visualizer There are other ways to build models in Cerius using the Analog Crystal Surface Interface Polymer and Amorphous builders You may have licensed some or all of these modules with your configuration of Cerius The tutorials in the Cerius Tutorials Materials Science and Life Science demonstrate the use of some of these sketchers Below is an illustration of the Sketcher control panel The Sketcher provides tools for mouse driven sketching editing an
176. column in a table However you can copy a model column from a table generated by another Cerius module such as QSAR into some other table Copying models from Copying columns from one table to another is essentially the same other tables as copying columns from one part of a table to another part of the same table Copying moving and clearing information 350 Cerius Modeling Environment April 1999 Modelsin tables The tables need not be displayed in the same table window How ever if they are being handled by the same table manager the table whose column s are being copied needs to be displayed as the current table Specifying the current table and then the other table needs to be made current in order to paste the column s into it The data type of the newly pasted column Assigning data types is automatically set to the model type Setting up calculations on models Accessing the tools Automated model calcu lations Since it can be tedious to set up mathematical expressions includ ing model references by hand Binary model operators Cerius can calculate certain properties and automatically insert them in a table column The models you are working with must be present in computer memory and at least one of them must be displayed in the model window Select the Data Atomistic Properties menu item from the TABLE card to access the Tabulate Atom Properties control panel If the table contains more than on
177. computer memory or you can remove all except those that are currently displayed Related information You can completely reinitialize Cerius by starting a new session Starting a new session Selecting graphs Selecting and displaying graphs and data sets Selecting which data sets to display and edit for display are discussed above Accessing the tools Select the Gallery Expert Functions menu item from the GRAPHS card to access the Graphs Expert Functions control panel Alternatively click the Expert Functions pushbutton in the Gallery Manager control panel to access the Graphs Expert Functions control panel Deleting all invisible First make sure that all graphs Selecting and displaying graphs and graphs and data sets data sets Selecting which data sets to display and edit that you want to keep are currently displayed in the Cerius2 Graphs window To remove all undisplayed graphs and data sets click the CLEAN pushbutton in the Graphs Expert Functions control panel 308 Cerius Modeling Environment April 1999 Deleting all graphs and data sets Additional information Managing graphs To delete all graphs and their data sets from both display and memory click the Reset menu item on the GRAPHS card Please see the on screen help for details on the functioning of each control in the Graphs Expert Functions control panel Saving graphs Important Related information Accessing the tools Saving graphs to
178. contained in the other sections of this documentation set Starting C erius 1 Preparing a work area Starting in your home directory you should first go to or make a sub directory in which to run this tutorial Do this by entering for exam ple the following at your system prompt 6 Cerius Modeling Environment April 1999 If nothing happens Starting C erus gt cd gt mkdir CeriusIntro gt cd CeriusIntro 2 Starting Cerius Enter at your system prompt gt cerius2 Cerius is a large program and it takes a few moments for it to load and appear on your screen Additional information on starting Cerius can be found under Starting Cerius2 If an outline of a window attaches to your cursor instead of being placed on the screen use the mouse to move the outline to the upper left corner of your screen and click there to place a large black window labelled Cerius2 Models It s possible that Cerius was installed so that you need to use some other command to start it at your site Please ask an experienced user at your site or your aaa administrator for this information If you installed Cerius and can t start it please see the Cerius Installation and Administration Guide and the Cerius release notes for troubleshooting information If after this you re still having trouble please contact MSI s Customer Support for example by sending email to support msi com 3 Getting
179. controls and then select the PRINT button If nothing happens Please ask an experienced user at your site or your system administrator how to access your printer s Contolling the 3D display 35 Depth cueing Depth cueing gives an impression of 3 dimensionality by causing the atoms that appear to be closest to the viewer you to appear brighter and those farther away to fade into the background You may want to adjust or turn off this feature Select the View Graphics menu item When you drag the cursor down to the Graphics item a pullright menu appears Continue dragging the cursor to the right and then down and release the mouse button over the View Graphics Depth Cueing menu item In the Depth Cueing control panel click the control on the Depth Cue Factor slider and drag it to the right The Depth Cue Factor slider and entry box now look like 42 Cerius Modeling Environment April 1999 Controlling the 3D display Depth Cue Factor You can also change the depth cue factor by entering a number in the Depth Cue Factor entry box A depth cue factor of 1 turns depth cueing off Setting it to zero results in extreme depth cueing the atoms farthest away from you will prob ably appear black Now set the Depth Cue Factor to some value less than 1 0 When the depth cue factor set to some value less than 1 you can use the Far Distance and Near Distance sliders t
180. cript file and enables more flexibility than RayTrace in defining the output PSYCHO reads atom and bond information and can generate color or gray scale images of spheres cylinders and polyhedra and can label atoms with any text strings PSYCHO also plots any isosurfaces that are present on the model such as orbitals although this cre ates significantly larger output files The final PSYCHO image is generally similar to the image in the Cerius model window although it does not include for exam ple bond orders hydrogen bonds custom pen colors or custom lighting effects When you render a PSYCHO image Cerius creates a PSYCHO input file default name C2Psycho dat and then runs PSYCHO with appropriate options PSYCHO reads the input file and creates a PostScript file default name C2Psycho eps or C2Psycho ps which by default is automatically previewed on your machine s PostScript previewer If you like what you see you can then send the PostScript file to your PostScript printer through your pre viewier or via the Cerius File Print menu item Printing models and graphs The Cerius PSYCHO control panels also give you access to the PSYCHO input file and options so that you can experiment with more complex PSYCHO renderings Select the View Rendering menu item to access the Render Models control panel Click the Preferences pushbuttons on that control panel to access the Psycho Preferences and Raytrace Pref
181. crystal van der Waals surfaces for models Model surfaces Atom and bond display styles Displaying surfaces Surfaces style and transparency Cerius Modeling Environment April 1999 217 7 Geometry Analysis You should already know The basics of starting Cerius and using its interface are demon strated in Introducing Cerius2 and described in The Cerius2 Interface You need to know how to build Basic building and or load Load ing model structure files models and should know how to select atoms in model s Selecting atoms and groups of atoms If your session contains several models you should know how to specify the current model Specifying the current model or select atoms in more than one model simultaneously Selecting atoms in several models Measuring models Why read this section Finding information Accessing the tools Display of measurements Removing displayed measurements You can measure distances angles planes torsions and inver sions for the atoms in a model and display these measurements in the model window or the text window This section includes information on measuring Distances Angles Planes Torsions Inversions Access the Measurements control panel by selecting the Geome try Measurements menu item in the main control panel s menu bar The calculated measurements are represented in the model win dow by lines and labels These are automatically updated wh
182. ct a range of contiguous models and or lt Ctrl gt click to add a noncontiguous model name Selected model rows are highlighted To deselect models lt Ctrl gt click to deselect individual models or simply click to start again with a single model The mouse button and keyboard combinations for selecting and deselecting model names which are the same as for selecting file names from file selector list boxes in control panels are described under Mouse actions Mouse operations are also described in the on screen help see On screen help for the model manager Contolling model visibility and the display mode Which models are visible When you have several models in your Cerius session you may want to view only the current model or you may also want to view one or more of the noncurrent models You may display them in individual model window panes or overlay them all in the main model window Use the visibility indicators square buttons to the right of the model names to control which models are visible Click one or more of the visibility indicators to toggle the mod els between being visible cyan pyramidal visibility indicators and hidden empty visibility indicators You can also Cerius Modeling Environment April 1999 203 6 Managing Modelsand Sessions How they are displayed Examples Show all models or all selected models by clicking the set to visible button on the top row of the model
183. ction mode 149 159 selection scope defined 162 selection tool 26 159 selections 46 session contents 213 loading 213 214 repeating 376 379 resuming a saved 213 saving the current 212 snapshot 377 session definition 212 set to definition 132 SHELX file format 427 single fiber diffraction patterns 295 sketch mode 152 Sketch with tool 11 152 Sketcher control panel 149 150 151 154 156 157 165 171 178 251 and periodic systems 191 Sketcher Template control panel 154 156 slices 372 slider 15 Sort Table control panel 361 363 sorting models current 206 current tool 206 ID tool 205 model ID number 205 name tool 206 names 206 visibility 206 visibility tool 206 spectra 266 specular light defined 280 Spotlight Settings control panel 286 spotlights 280 286 aiming 286 direction of illumination 286 jagged edges 287 position 286 width 286 spreadsheets 311 starting Cerius2 7 128 status windows 143 Stereo control panel 289 290 stereo viewing 289 cross eyed 290 Cerius Modeling Environment April 1999 447 Crystaleyes stereo hardware and glasses separation 290 Stereo View 289 stereo pair viewer 289 stopping a process 143 Strang J 6 399 Stretch tool 171 structure accuracy 20 optimization 20 trace 255 structures databases of 199 Style Preferences control panel 251 252 253 254 255 258 259 substitutional disorder 184 superconductors 253 superimposing models 239 surfaces 191 369 blende
184. ctions Select the View Graphics Projection menu item to access the Projection control panel Cerius Modeling Environment April 1999 257 8 Viewing and Displaying Models Adjusting the projection Additional information Choose the desired projection method from the control panel If you choose PERSPECTIVE you can specify the projection angle by entering a number in the Angle entry box Alternatively you can toggle the projection method by pressing lt F3 gt on the keyboard The perspective angle can be changed by dragging the mouse in the model window while holding down lt Shift gt and lt Alt gt and the middle mouse button Please see the on screen help for details on the functioning of each control in the Projection control panel Resolution and graphical quality Object resolution Line widths for bonds Graphics quality The balls ellipsoids and cylinders produced by the various dis play styles are represented on screen as multifaceted polyhedral facets for balls and ellipsoids and prismoidal facets for cylin ders A small number of facets used to draw an object results ina fast but coarse display Large numbers of facets improve smooth ness and specularity but at the expense of drawing speed The default value usually provides a reasonable compromise between display speed and resolution Although the actual number of facets used is determined by the size of the object being represented you can
185. cular Simulations native Cerius format for graphs TBL Molecular Simulations native Insight II format for graphs Documentation can be found elsewhere in http www msi com support Xy and con files Molecular Simulations old format for graphs Note The format descriptions in this appendix detail only what Cerius actually loads or saves which may not be all types of data stored in nonMSI files Structure files MSI The MSI Cerius native file format the default for loading and sav ing in the Cerius environment is extremely flexible This format default extension msi can hold all the information in the Cerius data model necessary to describe the attributes of a model The MSI file format is not designed to allow easy manual creation or editing However you can easily read it if required An exam ple file for an methane model is comments in bracketed italic type are not part of the file 416 Cerius Modeling Environment April 1999 Struc ture files MSI CERIUS2 DataModel File Version 2 0 1 Model 1 is the object ID Model is the object type and delimits model data A C Label methane A attribute tag C string type attribute 2 Atom 2 is the object ID Atom is the object type and delimits data for first atom A I ACL 1 H A attribute tag I integer type attribute A F Charge 0 028 F floating point type attrubute Charge is the nameof the attribute the followin
186. cur any number of times for different data sets within the ODB Sequenced in plotting order that is in reverse precedence gt GALLE RY METHOD GRAPH name version Any graph ODB within the file These may occur any number of times for different graphs within the ODB Sequenced in plotting order from top left row by row Tmnination record This is normally the last record of the file It is of the form gt END Cerius Modeling Environment April 1999 433 D File Formats Xy and con files Versions of CERIUS prior to CERIUS3 2 used different file formats for one and two dimensional data XY file extension xy for 1D data Stores xy graph data in a sequence list of x and y values CON file extension con for 2D data Stores data points as a function of two fixed range and interval variables x and y These two formats can be loaded into Cerius but files cannot be saved in this format All graphs are saved in the current grf for mat File documentation at our website The formats of these files are documented at our website in http www msi com doc car mdf arc cor tbl 434 Cerius Modeling Environment April 1999 Index tool 39 tool 32 3D Sketcher 149 A actinides 182 action buttons 131 140 Add Atom control panel 153 188 Added Atom Temperature Factors control panel 188 189 190 adding R groups 13 Align Atoms control pan
187. d car mdf files Control of the model c leaning function Specifying default behav ior of the clean function The default mode of operation of the cleaning function is as described under Refining the conformation However you may want it to function differently You can specify the mode of operation of the cleaning function the number of cycles performed for one shot cleaning which atoms are to be cleaned and which atoms are to be taken into account during the clean Click the Preferences pushbutton near the bottom of the Sketcher control panel to access the Cleaner Controls control panel 190 Cerius Modeling Environment April 1999 Additional information Other builders With this control panel you set preferences to Optimize the positions of all atoms in a model during cleaning or only those of selected atoms Take into account the interactions of all or selected atoms Optimize for a specified number of cycles one shot each time the CLEAN pushbutton in the Sketcher control panel is clicked or continue optimizing for as long as the mouse button is kept depressed after clicking the CLEAN pushbutton Watch the progress during one shot cleaning or update the view of the model only after cleaning is finished Clean continuously i e after every sketch operation without needing to click the CLEAN pushbutton Please see the on screen help for details on the functioning of each control
188. d atom selection 0 0 0000 e eee ee 163 Basic editing enra asta aenea a E ERANT 164 Changing atoms and their bonding types 165 Changing the element type n a nn nnnnnnnn 165 Changing the formal charge 00 167 Changing the bond type 00 0 nnno 167 Chan ing the hybridization and adjusting the valence 1 Cerius Modeling Environment April 1999 vii Editing the structure 1 6 eee eee 169 Deleting atoms and bonds 005 170 Duplicating parts of amodel 171 Examining and changing bond lengths 171 Examining and changing angles 172 Examining and changing torsions 173 Inverting about an atomic center 174 Translating and rotating atoms 175 Aligning and positioning atoms 176 Refining the conformation sess rsrsrsrs 178 Advanced building and editing 00 178 Editing element and bond attributes 179 Element properties 0 0 0 0 cece eee eee 179 Bond properties 66 c eee ee 181 Hydrogen bonds 00 c eee eee ee 183 E substitutional disorder 184 Introducing positional disorder 4 185 Temperature factors n eee eee 186 Specifying temperature factors 188 diting temperature factors 005 189 Loading and saving temperature factors 190 Control of the model cleaning function 190
189. d cleaning of models The operation of the Sketcher is modal that is the function of the left mouse button in the model window is determined by which icon is currently selected in the Sketcher control panel The default setting is to have the Selection mode icon highlighted This allows normal Cerius operation with the mouse button selecting atoms just as in the previous tutorial It is a good habit to always highlight the Selection mode icon before closing the Sketcher con trol panel Cerius Modeling Environment April1999 63 3 Tutorials Selection Mode icon Template icon _ P Sketch with Edit j Element e RA Hydrogen HADUUST Draw with Hydrogens Ti phenyl Templates J o ol Stretch Pay Angle IE o i 5 o Fuse S Connect H CLEAN Preferences Edit Hybrid AUTO EditBond SINGLE Edit Formal poj Charge AUTO Twist td Invert Delete X Delete Atom Bond Summary of tutorial The tutorial is divided into five short exercises A Building cyclohexane and saving the structure to file B Converting cyclohexane into the boat conformation C Editing cyclohexane to make benzene D Editing benzene to make phenol E Building xylene from template fragments Step by step tutorial This section takes you through a series of short progressive exercises designed to familiarize you with some basics of the Sketcher A Buildin
190. d dis play Click the top icon It overlays all currently visible models Return to border display mode by clicking the bottom icon Click the filled blue box on the bar above the Model Man ager list All models should now be displayed Click the adjacent empty box icon Only the current model is displayed Click the Name button immediately above the list Cerius Modeling Environment April1999 81 3 Tutorials This orders the models according to the first letter of the model names This is case sensitive names beginning with uppercase letters are listed before those beginning with lowercase letters Try clicking on the ID A and Visible buttons to sort models in other ways 0 Mods O DOLO lame butane cyclohexane napthalene phenol xylene Make napthalene the current model Click the icon above the Model Manager list and choose the OK button when prompted by the dialog box This deletes the model Make cyclohexane the current model Click the icon and choose the OK button when prompted by the dialog box This clears the model leaving it in the list but removing all data from it 82 Cerius Modeling Environment April 1999 Managing Modelsand More B Making picric acid from phenol tansfening data between model spaces In the following steps you learn how to
191. d for editing existing MolEN files Only users of MolEN can load and save files of this type The files atoms xyz and master par must be present in the direc tory where the files are stored Any xyz files may be loaded into Cerius but MolEN files saved by Cerius are named cerius xyz Only atom information can be saved from Cerius changes in symmetry or crystal cell dimensions cannot be saved MOPAC The MOPAC AMPAC Z matrix file format is the data input stan dard for the MOPAC and AMPAC quantum mechanical programs The default file extension for MOPAC files is pac Model structures are stored as internal coordinates using Z matrix format that is bond lengths bond angles and torsion angles rather than Cartesian coordinates that is x y z positions Although certain connectivity information is included MOPAC files do not store true bonding data If required after loading bonding can be recalculated using the Bond Calculation controls in the Edit Connectivity and Bonding control panel Atomic charges are optionally stored Because no crystal or surface infor mation is stored MOPAC files are suitable for storing only nonpe riodic structures The principal advantage of the internal coordinates system over a Cartesian structure description is the ease of creating structures from known bond length angle and torsion data The first three records are text Record 1 is reserved for MOPAC key words and records 2 and 3 are
192. d history in the text window Please see the on screen help for details on the functioning of each control in the Command Tracing control panel Some additional control over command logging and history is accessible via the Customize Environment control panel Accessing the tools Contolling Cerius from scripts Finding information Cerius enables you to play back command scripts containing command strings control syntax and optionally additional Tel commands The commands in the script are processed as though they were being generated in real time by the Cerius interface triggering the appropriate actions Command logging and scripting utilities enable you to record Cerius commands Recording commands into script files and play them back at a later time Command scripts are often based on Cerius log files which can be used unmodified to repeat a previous session Alternatively you can supplement a log file with Tool Command Language Tcl statements to produce responsive program like command scripts that can be used to drive Cerius and its applications In addition you can write command scripts completely from scratch This section includes information on Playing back scripts and log files Starting Cerius2 with a command script file Cerus Modeling Environment Apnril 1999 379 13 Scripts and Licensing Related information You should already know To learn more about using Tel to enhance script
193. d transparency 279 comparing 225 Connolly 223 contact 223 mapping a property onto a surface 371 matte 280 284 288 memory requirements 225 partial 223 printing 288 screen transparency 279 shiny 280 284 288 slices 372 solvent accessible 223 transparency 278 true transparency 279 van der Waals 223 SYM NUM 243 symmetry 34 Table Groups control panel 354 355 356 360 Table Manager window 314 Table Properties control panel 328 329 330 331 332 333 335 337 Alignment 328 Column 331 332 Datatype 329 Derivation 335 336 Format 330 Grid 333 Heading 331 333 Row 331 333 table window 314 and control panels 316 cell edit window 321 335 336 choosing among several 316 current cells 316 current table 314 current table tool bar 315 illustration 314 sections 315 table manager 314 table manager tool bar 315 tables 330 alignment 328 and control panels 316 ASCII files 319 automatic expansion 326 banners 331 Boolean 330 calculations 335 349 cancelling an edit 322 categories 330 cell information 321 changing values 321 chemical formulas 331 chemical names 331 clearing 322 323 324 clipboard 323 closing 327 column headings 332 column numbers 331 column width 332 columns selecting 322 control panels 316 copying values 322 creating 317 current 316 320 current cell 321 cursor movement 321 cursor wrap 326 cutting values 323 324 data types 329 334 data types example 329 decimal pl
194. data from a Cerius2 session The basics of starting Cerius and using its interface are demon strated in Introducing Cerius2 and described in The Cerius2 Interface Graphs in Cerius are produced as output from calculations in var ious other application modules How to set up and run the appro priate calculations are discussed in the documentation for the relevant application modules The tools for handling graphs are accessed from one of the decks of cards in the main Visualizer control panel To access the Graphs module click the deck selector see also Access to application mod ules and choose TABLES amp GRAPHS from the list that appears Then click the title of the GRAPHS card to bring it to the front The deck of cards menu area should now look like this 292 Cerius Modeling Environment April 1999 Additional information Creating graphs Why read this section Finding information Creating graphs Please see the on screen help for details on the functioning of each control on the GRAPHS card Ordinarily graphs are created and displayed automatically as the result of some calculation in a Cerius application module If you are dealing with such graphs you do not need to read this section However you may want to create a graph from a blank user graph and selected data Or you may want to import and graph data from a file output by an Insight II module This section includes information on S
195. dditional information ment characters in the Replace entry box and assure that the asso ciated popup is set to Text To delete found material from the cells containing them set the Replace popup to Null Cells Then initiate the search by clicking the FIND amp REPLACE push button see Initiating the search Ordinarily found cells are just highlighted after the search is complete However you may also View only the rows and columns that contain the found cells by checking the View Results check box Additional information on viewing subsets of a table starts under Viewing subsets of a table and or Define the rows and columns that contain the found cells as a group by checking the Save Results check box and entering a group name in the associated Group entry box Additional information on groups in tables is in Grouping table information To simply search for the desired information click the FIND push button in the Find Cells control panel To search for information and replace it with the specified text click the FIND amp REPLACE pushbutton in the Find Cells control panel Please see the on screen help for details on the functioning of each control in the Find Cells control panel Viewing subsets of a table Finding information You can collapse the view of a table so that only a designated set of rows or columns is displayed You can toggle between viewing the full table and viewing the design
196. del See Model display style Labels and Set ting position and orientation Atom selection controls Use these tools to control atom selec tion See Selecting atoms and groups of atoms Cerus Modeling Environment April 1999 135 4 The Cerius Interface Cascade control panels Click to reorganize all open control panels into an ordered cascade which helps prevent screen clutter Close all control panels Click to close all open control panels Menu card search Click to access the Menu Card Search con trol panel which enables you to search for words in the deck of cards menu hierarchy and in the menu bar menus Menu card searching The model manager The model manager enables you to control the selection editing and saving of models in the Cerius modeling environment 1 Modell The model manager is described fully under Basic model manage ment tasks Deck of cards menu The deck of cards menu on the main control panel provides easy access to application modules and their controls 136 Cerius Modeling Environment April 1999 Access to application modules Customization Using the main control panel Directional button oa Ea Deck selector SURFACE BUILDER CRYSTAL BUILDER Cards The exact appearance of the deck of cards menu depends on which application modules you have purchased Each module that is added to the Cerius interface is represented by a menu card
197. dicated in the model window A dotted line indicates what distance was measured Information on examining and changing bond lengths is con tained under Examining and changing bond lengths Angles Measuring angles To measure the angle involving any three atoms you use the Angle tool You can use it in two different ways Cerius Modeling Environment April 1999 219 7 Geometry Analysis Select the Angle tool and then pick atom triplets whose angles you want to measure These atoms need not be bonded to one another The angle s in degrees are indicated in the model win dow or Select any number of atoms and then double click the Angle tool The angles in degrees of each existing valence angle con necting three consecutively bonded selected atoms are indi cated in the model window Dotted lines indicate what angle was measured Related information Information on examining and changing angles is contained under Examining and changing angles Planes Measuring angles defined To measure the angle between any two planes you use the Plane by two planes tool You can Select the Plane tool Pick three atoms that define the first plane and then three that define the second plane or Select three atoms that define the first plane and then three that define the second plane Then double click the Plane tool The angle between the two planes in degrees is indicated in the model window as well
198. ding information Cerius can hold many models at one time each in its own model space This section tells you how to work with several models that are present simultaneously in the same Cerius session The num ber of models allowed depends only on your computer s memory limitations This section includes information on Basic model management tasks Moving models between model spaces Cerius Modeling Environment April 1999 199 6 Managing Modelsand Sessions Related information Building models is explained in Building Models and demonstrated in Introducing Cerius2 Loading models is discussed under Loading model structure files You should already The basics of starting Cerius and using its interface are demon know strated in Introducing Cerius2 and described in The Cerius2 Interface Basic model management tasks Why read this section When you have several models present simultaneously in the same Cerius session you need to know how to make a model be current so you can work with it You may also want to know how to display one or more models name models open a new model space in order to load or build another model etc Finding information This section includes information on Creating clearing and deleting model spaces Specifying the current model Selecting model spaces Controlling model visibility and the display mode Renaming models Sorting model table entries The model manager The mod
199. display the Sorption Loading Plot graph 108 Cerius Modeling Environment April 1999 Managing and Modifying Graphs Open the Save Graphs control panel by choosing File gt Save Graphs from the Graphs card Type two_graphs grf into the filename text box and click the Save button A confirmation message like the one shown below is written to the text window Saving Gallery File two_graphs grf Saved GRAPHS file Delete graphs from the Gallery Choose Reset from the Graphs card and choose Re initial ize Graphs from the dialog box to confirm the reset Reset deletes all graphs from the Gallery Manager and returns all Graphs controls to their default settings The Gallery and graph window should now be empty Load the saved file of multiple graphs Open the Load Graphs control panel by choosing File gt Load Graphs from the Graphs card You may have to move up several directories to return to your working directory where the two_graphs grf file is located Load back the two_graphs grf file Cerius Modeling Environment April 1999 109 3 Tutorials F Creating new graphs and using expert functions Clear Data Placement amp Keep Same In this final section of the Graphs tutorial you create a new User Graph and copy datasets from other graphs onto it You also learn how to use the Expert Functions Clean Data Placement and Keep Same
200. dy occupied model space all the contents of that model space are considered to be one model Loading the model file s There are several ways of selecting and loading the desired file s To load a single model file double click its name in the file selector list box or Select its name file selector list box the name becomes high lighted and then click the LOAD button or Enter its name in the filename text entry box Enter means to type in the name and then press lt Enter gt or click the LOAD button To load several model files simultaneously select their names in the file selector list box and then click the LOAD button To select several model files click the first filename and then drag to select several contiguous filenames and or lt Shift gt click to select a range of contiguous filenames and or lt Ctrl gt click to add a noncontiguous filename Selected filenames are highlighted To deselect filenames lt Ctrl gt click to deselect individual filena mes or simply click to start again with a single filename The mouse keyboard combinations for selecting and deselect ing filenames which are the same in any control panel that con tains a file selector list box are all described under Mouse actions Example A tutorial example of loading models can be found in Reading in additional models 198 Cerius Modeling Environment April 1999 Additional controls Additional information Models
201. e In thisexample much of the Connolly surface is equivalent to the van der Waals surface Where the probe contacts only one atom of the model the Con nolly surface is equivalent to the van der Waals surface of the model Where the probe contacts two or three atoms simulta neously the Connolly surface is equivalent to the van der Waals surface of the probe Figure 2 The resulting surface represents the solvent accessible surface of the molecule assuming that a mole cule of solvent is a sphere with the same radius as the probe Accessing the tools Access the Connolly Surfaces control panel by selecting the Geom etry Connolly Surfaces menu item in the main control panel s menu bar You use this control panel to calculate and display Con nolly surfaces involving all or selected atoms in your model You can Calculate a surface for the entire model Set both Atoms to be surfaced and Atoms in calculation to ALL 224 Cerius Modeling Environment April 1999 Calculating Connolly sur faces Displaying Connolly sur faces Tip saving and loading Con nolly surfaces Model surfaces Calculate a surface that surrounds only selected atoms Set both Atoms to be surfaced and Atoms in calculation to SELECTED Calculate a partial surface Set Atoms to be surfaced to SELECTED and Atoms in calculation to ALL Set the Calculation Preferences controls in the Connolly Surfaces control panel as desired then click the
202. e which people have a particular feature checked out When you check out a feature the indicated total number of tokens by your name is increased To manually reserve check out one floating licence for the selected module click the name of the selected module in the Available Licenses list box or click the CHECK OUT pushbutton To manually reserve several token licenses for a specific feature user or machine please see the Cerius Installation and Administra tion Guide on using an options file To return check in a license that you have checked out manually for a selected module but are finished using click the name of the selected module in the Available Licenses list box or click the CHECK IN pushbutton Please see the on screen help for details on the functioning of each control in the License Management control panel For additional information about a particular license i e when it expires and what machine is serving it click the License pushbut ton For more information about licensing including the differences between token and floating licenses and between features and modules and license management please refer to the Cerius Installation and Administration Guide 384 Cerius Modeling Environment April 1999 Running application modules extemally Running application modules extemally Uses of remote servers How it works External application facilities enable you to manage Cerius appli catio
203. e 24 Comparison criteria in Cerius table searches Relational operator lin Description Search cellsforan exact match to the entered characters Search cellsforan approximate match to the entered characters using a tol erance value specified in the Tolerance entry box Search cells for items that do not match the entered characters Search cells for items that are greaterthan the entered characters Search cells for items that are greaterthan or equal to the entered charac ters Search cells for items that are less than the entered characters Search cells for items that are less than or equal to the entered characters Fortext comparisons search cellsto determine whetherthe entered charac ters is contained within a cell value In a replace operation only the matching content of the found cell s is replaced with the specified replacement characters Forexample suppose the entered characters bed isto be replaced with the value BCD If the string AbcdEF is found it is replaced with ABC DEF not simply BCD Fortext companisons search cellsto determine whetherthe entered charac tersare nofcontained within a cell value Mhat is the characters you entered in the Find entry box 358 Cerius Modeling Environment April 1999 Viewing subsets of a table Changing the contents of To replace found material with something else enter the replace found cells Where to put the results Initiating the search A
204. e Group command and choos ing the desired group from the Group pulldown Please see the on screen help for details on the functioning of each control in the Table Properties control panel Assigning data types Note Accessing the tools Assigning data types You can assign or reassign data types to selected column s or the current cell The data type determines whether content that is sub sequently entered in that cell or column is interpreted as real num bers Booleans text etc The type interacts with the cell format Setting display formats to affect how the cell content is displayed For example when false is entered into a weakly typed character or real number type cell it is displayed and interpreted merely as text and therefore evaluates to True if the format is subsequently changed to True False since it is true that the cell has content However when false is entered into a Boolean type cell it is inter preted and displayed as 0 00 if the format is set to a floating point real number or as False if the format is set to True False If a table generated by a Cerius application module contains strongly typed cells you cannot change the data type for those cells To assign or reassign data types access the Table Properties control panel as above see Accessing the tools and set the Properties popup to Datatype to access the Datatype controls To assign a data type to the selected column s the curren
205. e Manager window Creating a new table You can create a new empty table and fill it in by hand this sec tion or you can create a Cerius table from an ASCII text file Importing an ASCII text file into a new table Cerius Modeling Environment April 1999 317 11 Working with Tables Creating anew empty table To create a new empty table either Click the NEW tool in the table manager tool bar for illustra tion see Accessing the tools of the table window or Select the File New menu item from the TABLES card The new empty table appears as the current table in the main section of the table window Loading and reloading tables Loading saved table files Reloading the current table Tables that have been created and saved to a file Saving a table can be loaded into a subsequent Cerius session In addition you can revert to the previously saved version of a table file if you want to discard changes that you made since the last time you saved the table To load a table you need to access the Open Table control panel Click the OPEN tool in the table manager tool bar or Select the File Open menu item from the TABLES card Using the file browser in the control panel to navigate the directory structure is fairly intuitive The procedure is described under Load ing model structure files To revert to the previously saved version of the current table Click the REVERT tool in t
206. e add model space tool in the model manager The new model space s name is added at the bottom of the model table Cerius Modeling Environment April1999 201 6 Managing Modelsand Sessions Clearing a model space Deleting a model space You may want to replace an existing model with a new one or per haps realize you ve built or loaded an incorrect model Clearing a model space removes the model but allows its now empty space to remain in the model manager To clear a model space click the clear model space tool in the model manager If no model space s are selected Selecting model spaces the current Specifying the current model model space is cleared For many models you can also select Selecting atoms and groups of atoms all the atoms of the current model and delete them Deleting atoms and bonds to clear the current model space Nonatomic information if any is not removed by this method If you want to delete both the model and the space that contains it click the delete model space tool in the model manager If no model space s are selected Selecting model spaces the current Specifying the current model model space is deleted The last remaining model space cannot be deleted Example A tutorial example of adding and deleting model spaces is found under Managing multiple models Specifying the current model Setting the current model Example The current model is the one to which display c
207. e aniso tropic temperature factors Uj If the atomic vibration is isotropic then H reduces to the form x I and requires just one number the isotropic temperature factor Uj to describe it 2 2 OF Eq 2 Temperature factors are commonly used to describe the effect of vibration on X ray electron and neutron scattering For the first order amplitude of scattering from an atom at q ha kb Ic in reciprocal space the scattering amplitude is multiplied by e 27qHq anisotropic Eq 3 e727 x2 q2 isotropic Several different though equivalent ways of describing the tem perature factors exist Cerius can read temperature factors in sev eral formats see Loading and saving temperature factors Sometimes the vibration is described in terms of a crystal lattice coordinate system a b c rather than a Cartesian one If an atom has coordinates x y z with respect to the Cartesian axial system and u v w with respect to the lattice system so that xityjt zk uat vb we Eq 4 then x y z and u v w can be interconverted by multiplying by a matrix A where x y z A u yw Table 3 shows the relationship between the different temperature factor forms and the way in which they modify the scattered amplitude Internally Cerius stores the atomic vibration matrix H Cerius stores isotropic and anisotropic temperature factors for every atom You decide which of the two types to use for calculation or display
208. e appropriate red green and blue sliders or the entry boxes below them to set the proportions of red green and blue To return the Ambient Diffuse and Specular components of your light source to a neutral color click or adjust the appropriate Gray control Cerius Modeling Environment April 1999 283 9 Enhancing Model Display How it works Directional lights Accessing the tools In general the ambient component affects the contrast how flat or 3D the model appears and the relative amounts of the specular highlighting and diffuse components affect how shiny or matte the object appears see Concepts for more details Directional lights give overall illumination of a scene from a par ticular direction Concepts To set up a directional light located at infinity click the Posi tion pushbutton in the Lighting control panel to access the Lightsource Position control panel Select the Light is Directional control Changing the direction of You can change the direction from which the light illuminates the illumination How it works model by using any combination of the X Y Z Latitude and Lon gitude controls the Radius control is ignored since the a direc tional light is by definition located at infinity For example you can Illuminate from directly in front of the computer screen by set ting the X and Y directions to 0 and the Z direction to any pos itive number This is equiva
209. e atom to select it and deselect all others Or you can select several atoms at once Hold down the left mouse button and drag out a rectangle in the model window so as to enclose several atoms Drag out another rectangle to select a different group of atoms or one atom lt Shift gt drag to select an additional group of atoms lt Shift gt drag some already selected atoms to deselect them You can select or deselect all atoms at once Click the selection tool SELEC to select all atoms Click the deselection tool 2q to deselect all atoms Click empty space to deselect all atoms 26 Cerius Modeling Environment April 1999 What you can do with a model display 19 Measuring components of the model s geometry Select the Geometry Measurements menu item The Measurements control panel appears Click the Distance tool in the Measurements control panel The Distance tool looks like Click any two atoms A dashed line and a distance in angstroms are displayed on the model Most tools on Measurements control panel work similarly click the tool then click the required number of atoms If you need more information look ahead to Step 20 Clear the measurements Click the DELETE Measurements action button Definition Even though this button is small it is an action button as indicated by its blue color Cerius Modeling Envi
210. e distance between C12 and C16 and these atoms are not present in all the models calculated values are displayed only for those models that do have these atoms To input expressions into several columns simultaneously you can select more than the number of atoms specified above and then double click the desired tool This method does not for example calculate all distances among the set of atoms selected but the pairwise distances in the order in which atom pairs were selected To recalculate model expressions after changing the models for example after optimizing their structures click the RECALC but ton in the current table tool bar Checking the Guide check box gives you on screen help in the upper left corner of the model window on using the Tabulate Atom Properties control panel Please see the on screen help for details on the functioning of each control in the Tabulate Atom Properties control panel Saving tables containing models Saving a table Saving a table that contains models saves only the model ID with the table Structural data are not saved therefore structures are not displayed if you open that table file in a future 352 Cerius Modeling Environment April 1999 Grouping table information Cerius session If you want to also save the models you need to save the session Saving the current session Grouping table information Finding information Uses of named groups You should a
211. e in a deck click the right pointing arrow The same card may appear in more than one deck To change the order of cards in the deck click a card name in the right hand list box and click the up or down pointing arrow To remove a card from the deck click the card s name in the right hand list box and click the REMOVE pushbutton The card is still available in the Licensed Cards list box for inclusion in other decks if desired Any card deck configuration changes you make are immediately reflected in the deck of cards area of the main control panel Your changes remain throughout the current Cerius session To save your changes so that Cerius always starts up with your custom configuration click the SAVE CONFIGURATION push button in the Customize Menu Deck control panel When you click the SAVE CONFIGURATION pushbutton the current configuration of the deck of cards menus is saved to a file named decks in an MSlIguirc subdirectory in your home directory This file is automatically read whenever you start Cerius Cerius Modeling Environment April 1999 391 14 Customizing the Interface Additional information To set up different deck of cards configurations for use when you run Cerius for different purposes or projects simply create sepa rate directories and copy the MSIguirc subdirectory and its contents to the new directory Then change the decks file as described in Saving the new deck configuration If
212. e is normally overwritten when a new Cerius session is started however the contents of the current RUN LOG file that is the session log can be saved under another filename at any time Such files provide a snapshot of the session at a partic ular time You can also open a supplementary log file called a segment log file into which all generated commands are logged until this file is closed A segment log file enables you to create a log of only part of a session for example only that part of a session from which you want to create a command script Command logging to RUN LOG also continues regardless of whether a segment log file is open Select the Utilities Record Commands menu item in the main Visualizer control panel to access the Record Commands control panel To copy all the current contents of the RUN LOG file to a file with a different name change the filename in the entry box near the top of the Record Commands control panel if desired and click the Dump current Log contents action button To start copying commands into a supplementary log file check the Echo commands into file check box All subsequent com mands appear in both the RUN LOG file and the segment log file To discontinue copying commands into the supplementary log file uncheck the Echo commands into file check box If you want to record more commands into the same file later in your session simply check the Echo commands into file check box aga
213. e model column specify which one you want to refer to by choosing its name or number from the Molecule Column pulldown in the Tabulate Atom Properties con trol panel Several types of calculations are facilitated To calculate the charge on atoms select the Charge tool and click an atom in a representative model in the model window To calculate the distance between pairs of atoms select the Dis tance tool and click two atoms in a representative model in the model window To calculate the angle between three atoms select the Angle tool and click three atoms in a representative model in the model window Cerus Modeling Environment April1999 351 11 Working with Tables Tip Help Additional information To calculate the dihedral angle relating four atoms select the Dihedral tool and click four atoms in a representative model in the model window The correct mathematical expression is generated automatically and placed in an empty column in the table on its right side The calculated charge distance etc is displayed in that column The term representative model above assumes that all the models in the column have some structural moiety in common If for example you request the distance between atoms C1 and C2 and all models in the model column contain atoms labeled C1 and C2 then calculated values are displayed in all cells of the column containing the expression If however you request th
214. ead Only if the cell cannot be modified An asterisk if the cell is strongly typed and can thus contain data only of a certain type see Assigning data types For empty cells the default numeric data type is double an eight byte real number and the default cell format is a floating point number with two decimal places If you enter a number with more decimal places the displayed value is rounded to two places but the value is stored in the cell the way you enter it You can change the format and other properties of your entries as described under Table style and display Formatting and naming rows and columns are presented under Table style and display Applying mathematical expressions to col umns is discussed under Values and mathematical expressions Make the desired cell current by clicking it with the mouse or mov ing the cursor to that cell with the arrow lt Tab gt or lt Enter gt keys To replace the current cell s content with new content you can simply start typing while the cursor is anywhere in the table win dow To edit or replace the current cell s content select the cell edit win dow by clicking it or by pressing lt Shift gt lt Tab gt on the keyboard Then position the cursor as desired within the content of the cell edit window by clicking and or using the arrow keys and type the desired cell contents Until you enter the new content Entering your changes you can edit it in the cell edit w
215. ecular mechanics minimization the positions of the atoms in 120 Cerius Modeling Environment April 1999 Basic Molecular Simulation Minimization amp Dynamics the model are altered to find lower energy conformations of the molecule Open the Energy Minimization menu by selecting Run from the Minimizer card Minimize the Energy The Smart Minimizer works through a series of minimization algo rithms that have been found to give the most efficient minimization for molecular models Pick the Smart Minimizer with the right hand mouse button to read about the methods used With the options set as shown up to 500 iterations changes in the molecular model which reduce its energy will be carried out The minimiza tion will stop either at 500 interactions or earlier if a minimum energy structure is located Select the Preferences button to see the convergence cri teria used Select the Run button to minimize the energy Cerius Modeling Environment April 1999 121 3 Tutorials C Add water to the system 1 Create water molecules with the Sketcher If the 3D Sketcher menu is not still active open by selecting it from the Build pulldown menu Change the Sketch with element to oxygen and double click at five or six random locations around the glucose molecule This sketches five or six isolated oxygen atoms shown by default as small red stars Select the H AD
216. ed and com mand line options by entering it in the Command entry box You can access some less frequently used controls by clicking the Page Setup pushbutton in the Print control panel which causes the Page Setup control panel to appear Options on the Page Setup control panel enable you to adjust the presentation of the PostScript image to be generated You can also scale the image add legends and fine tune the output for maxi mum clarity The controls available in this panel depend on how controls in the Print control panel are set If you are printing the image in the model window you can choose to output in vector PostScript or screen dump raster format Vec tor PostScript images are device independent can be resized with out loss of display quality and can produce better quality output colors shapes and so on on a PostScript printer Raster images such as screen dump images may become distorted when they are scaled 260 Cerius Modeling Environment April 1999 Bitmap resolution for print ing graphs Previewing the output Printing or saving a Post Script file Example Additional information Printing models and graphs A vector PostScript file is often smaller than a screen dump file and as a result prints faster However if the image in the model window is very complicated or the display quality is high a vector PostScript file can be larger than a screen dump file and may take longer to pri
217. ed 271 crystals 191 210 438 Cerius Modeling Environment April 1999 CSSR file format 423 current cell defined 321 current table defined 314 cursor behavior 150 407 customer support 46 customization colors 268 Customize Environment control panel 164 379 396 397 Customize GUI Colors control panel 395 Customize Menu Deck control panel 390 391 392 Customized Atom Selection control panel 163 164 D databases structures 199 209 Davis T 399 deck of cards menu 133 136 decks card 133 Delete Atom tool 170 Delete Bond tool 170 Depth Cue Factor slider 42 depth cueing 42 factor 43 Depth Cueing control panel 257 depth cueing defined 257 deselect tool 26 deselecting filenames 198 diffuse light defined 280 dihedral angles 221 352 directional light defined 280 directories and initialization scripts 382 Cerius2 Models 199 Cerius2 Resources 428 creating 209 212 moving between 197 MSI guirce 391 392 394 395 newly created and file browsers 210 opening 197 run 197 387 startup 197 working 387 directory selector popup 197 disorder positional 185 substitutional 184 Disorder control panel 185 186 disordered structures 180 display border mode 204 enhancing 245 grid mode 204 overlay mode 204 resolution 258 Display Attributes control panel 244 250 251 252 253 255 256 258 259 278 279 display axes 231 clipping planes 256 Z axis 256 display mode tools 38 204 display modes 204 d
218. el Then click three contiguous bonded atoms The angle between them in degrees is displayed next to the angle in the model win dow when you click in empty space To change the angle click and 172 Cerius Modeling Environment April 1999 Precise change in angles Additional information Default angles Basic editing drag the cursor in empty space in the model window Dragging up and or to the right increases the angle dragging down and or to the left decreases it Angles in rings cannot be changed You can also modify angles by moving atoms manually Translat ing atoms manually You can examine angles between any three atoms with the Measurements control panel Angles To change an angle precisely select the Move Bond Geometry menu item to access the Bond Geometry control panel Please see the on screen help for details on using the controls in the Bond Geometry control panel to measure and change valence angles bond lengths and torsions and to specify which atoms are moved in the process You can also change angles in the course of translating Translating atoms precisely aligning or positioning Aligning and positioning atoms atoms to specified locations You can also examine angles between any three atoms with the Measurements control panel Angles You can implicitly control default valence angles through setting the hybridization state of the atoms involved Changing the hybrid ization and adjusting t
219. el 177 alkali metals 182 ambient light 43 280 ambient light defined 280 amorphous structures 191 analogous structures 191 Angle tool 172 219 angles between planes 220 changing 172 measuring 173 219 351 view 233 animation 241 building a sequence 241 frames 241 loading 241 model display 241 replaying 242 Animation control panel 241 242 anisotropic temperature factors 187 annotation arrows 245 circles 246 color 247 defaults 244 246 deleting 247 editing 246 font and style 247 hiding 247 line width 247 lines 245 moving items 247 rectangles 245 resizing 247 text 246 247 Annotation control panel 245 248 266 application modules accessing 137 external servers 385 independent processes 385 internal names 386 remote hosts 385 application preferences 213 214 arrow on control panel 149 arrow on menu card 137 arrows in display 245 Atom Selection control panel 162 atom selection controls 135 Atom Visibility control panel 255 256 atomic mass 179 180 atomic number 180 atomic radius 179 atomic vibrations 186 254 atoms adding groups 154 backbone 255 274 changing element 16 181 charge 181 351 close contacts 222 color 29 45 180 264 265 267 color coding 11 274 connectivity 210 coordinates 210 coordinates finding 164 copying and pasting 207 cutting and pasting 207 deleting 170 distances 219 351 illuminating 285 labeling 45 243 lone display style 33 252 Cerius Modeling Environment April 1999
220. el manager is part of the main control panel When a Cerius session is started with an empty model space the usual default startup the model manager looks like 200 Cerius Modeling Environment April 1999 Overlay mode tool Grid mode tool Border mode tool Add model space Sorting criteria Model ID number Cunent model indicator im soe Model name Visibility indicator Scroll bar Handling multiple models Delete model space Clear model space a Model count T Setto visible au F to invisible 0 Moes MP we 1_ gt Modell reed Model table Please see the on screen help for details on the functioning of each control in the model manager Additional information Creating clearing and deleting model spaces When do you need to add model spaces Creating an empty model space Model spaces are added automatically to accommodate models loaded from files or generated by application modules For instance when you use the Load Model control panel to read ina model from disk Loading model structure files the model is added by default to a newly created model space or if it is completely empty to the current model space However for example builders have no way of knowing when you may want to start anew model They therefore assume that you want to continue modifying an existing model until you inform them otherwise To add an empty model space click th
221. electing graphs to display To shift only selected data set s along the y axis select the Data Plotting Attributes menu item from the GRAPHS card to access the Plotting Attributes control panel Alternatively click the Plot ting Attributes pushbutton in the Graph Manager control panel to access the Plotting Attributes control panel To change the proportions of the graph window select the Gal lery Manager menu item from the GRAPHS card to access the Gallery Manager control panel For all other scaling or axis shifting tasks select the Graph Scal ing menu item from the GRAPHS card to access the Graph Scaling control panel Alternatively click the Graph Scaling pushbut ton in the Graph Manager control panel to access the Graph Scal ing control panel The controls available in this control panel depend on the type of graph you have selected for editing The name of this graph appears near the top of the Graph Scaling con trol panel The x and y axis ranges can be changed for x y and 2D Cartesian graphs The angle between the axes can be changed for 2D Carte sian graphs To explicitly set the range of values covered by the x and y axes enter values in the Min x Max x Min y and Max y entry boxes of Cerius Modeling Environment April 1999 301 10 Working with Graphs Changing angles in polar graphs Shifting a data set along the y axis Scrolling a graph Changing size or propor tions of a graph displ
222. electing named groups Please see the on screen help for details on the functioning of each control in the Table Groups control panel 360 Cerius Modeling Environment April 1999 Sorting table information Viewing search results Accessing the tools Viewing only search results Viewing the whole table Related information Additional information To view only the results of a search you need to request this while setting up the search criteria with the Find Cells control panel Click the FIND tool in the table manager tool bar or Select the Data Find menu item from the TABLES card You can specify that only the search results be displayed after a search Before starting the search Searching for information in a table check the View Results check box in the Find Cells control panel After the search is complete only the results are visible in the current table To view the entire table click the RESTORE VIEW tool in the table manager tool bar or select the Data Restore View menu item from the TABLES card The RESTORE VIEW pushbutton in the Table Groups control panel also works Conducting searches is discussed under Searching for information in a table Please see the on screen help for details on the functioning of each control in the Find Cells control panel Sorting table information You should already know Accessing the tools You can reorganize a table by sorting its rows on the bas
223. ell parame 6F11 5 ters lengths of axes a b c in and angles alpha beta gamma in degrees C ELLS 1X 615 Cell extension limits C ELLS Mina Maxa Min b Maxb Min c Maxc the number of rows of cellsto be added in nega tive and postive directions along the a b and c axes Ignored on reading On writing min set to 1 maxto 1 This ensures that model is extended in POLYGRAF ensuring any crystal bonding is not lost The following five record classes are present only in periodic files 10 XTLUNQ files with struc tures gener ated by POLYGRAF Crystal Builder only 11 FORMAT ATOM 12 ATOM or HETATM XTLUNQ 15 1X Fractionalcoordinatesand designator information XTLUNQ A5 1X A3 1X A1 atom number atom label residue name chain designator 1X 3F9 6 1X A5 must be uppercase orblank residue number fractional x 1X 213 F8 4 12 y and z coordinates atom type max number of covalent F6 2 bonds no of lone pairs atomic charge atom symbol code 1 dots 2 tetrahedron 3 octahedron 4 6 point jack 5 12 point jack 6 18 point jack atom symbol size in A atom symbol color hue value in range 0 360 FORMATATOM ATOM HETATM record format specification if not present the 3X A default format is used FORMATATOM format specifica tion for ATOM HEAM records ATOM HETATM Atomic coordinate and force field recordsforstandard groups 1X 15 1X A5 1X ATOM or HETATM atom num
224. en ever the model is modified enabling you to monitor the effects of manipulations as you perform them You can display all measurements in the text window by clicking the List measurements action button To remove all measurements from the display click the Delete measurements action button To temporarily hide the calculated 218 Cerius Modeling Environment April 1999 Example Additional information Measuring models measurements without deleting them check the Hide measure ments check box You can selectively delete measurements by selecting the appro priate measurement tool see below and then re selecting the atoms that were picked to calculate those measurements A tutorial example of using the Measurements control panel is found under Measuring components of the model s geometry Please see the on screen help for details on the functioning of each control in the Measurements control panel Distances Measuring distances Related information To measure the distances between atoms you use the Distance tool You can use it in two different ways Select the Distance tool and then pick atom pairs whose dis tances you want to measure These atoms need not be bonded to each other The distance s in angstroms are indicated in the model window or Select any number of atoms and then double click the Distance tool The lengths in angstroms of each bond existing between selected atoms are in
225. en atom is less than the distance criterion The angle between a potential donor a hydrogen and a poten tial acceptor is greater than the angle criterion distance criterion angle criterion Figure 1 Hydrogen bond criteria A hydrogen bond acceptor D hydrogen bond donor Editing hydrogen bonds Select the Build Edit H Bonds menu item to access the Edit Hydrogen Bonding control panel With this control panel you can calculate delete or make hydro gen bonds between all or selected atom pairs as well as set the color in which hydrogen bonds are displayed in the model win dow You can also enable automated recalculation of hydrogen bonds whenever for example the model s conformation changes Additional information Please see the on screen help for details on the functioning of each control in the Edit Hydrogen Bonding control panel Cerius Modeling Environment April 1999 183 5 Building Models Specifying how hydrogen bonds are calculated Additional information Calculating hydrogen bonds To define the criteria by which hydrogen bonds are calculated click the Preferences pushbutton in the Edit Hydrogen Bonding control panel to access the H Bond Preferences control panel With this control panel you can set the distance and angle criteria You can also specify the hydrogen bonding nature of an element i e whether it is a donor an acceptor either a donor or an acceptor or neither a donor
226. en help for details on the functioning of each control in the Sort Table control panel Graphing table infomation Related information You should already know Accessing the tools Specifying the data to plot on the y axis You can plot selected columns or rows as line graphs scatter plots or histograms Values in columns are plotted vs corresponding values in other columns or values in rows vs values in rows Editing Displaying and editing graphs and managing Managing graphs graphs are discussed in Working with Graphs How to access the Tables module is described under Accessing the tools How to select a table for display and editing Specifying the current table and how to make sure control panels are connected to the desired table window Keeping track of the current table are dis cussed above Selecting columns and rows is discussed under Selecting rows and columns To graph table contents you need to access the Plot Table control panel Click the graph tool in the current table tool bar or Select the Data Graph menu item from the TABLES card Ordinarily related data are contained in columns and the Y Axis popup should remain set as Columns Cerius Modeling Environment April 1999 363 11 Working with Tables Specifying the x axis Note Specifying the type of graph Titles and labels Generating the graph To plot all data contained in one or more columns select the col u
227. en the Graph Scaling control panel Graph gt Scaling from Graphs card and set the scale of the X axis to 300 600 and the scale of the Y axis to 1 3 2 0 114 Cerius Modeling Environment April 1999 Managing and Modifying Graphs Open the Plotting Attributes control panel Data gt Plotting Attributes from Graphs card and set the Color popup to your favorite color Set the following option values in the Graphs Expert Func tions control panel Data Placement Additional Graph Keep Same Graph Axes On Keep Same Plot Attributes On Reload the file Cerius2 Resources EXAMPLES data EM_ MM_Emix grf Because the Keep Same options are toggled on the scale and plot attributes for the new graph are not the ones stored in the file but instead they are the same as the previous version of the graph o H x Pibecetnte xy SO 20 fherain 79 Enix Fit vl Enix Fit v Cerus Modeling Environment April 1999 115 3 Tutorials 7 Exit or continue to new tutorial If you are going to continue immediately with another tutorial Re initialize the program by selecting New Session from the File pulldown menu and choosing the Confirm button on the Re initialize dialog box Re initialization resets all the Cerius control panels to their original defaults Alternatively if you want to stop now Choose Exit from the File pulldown menu to quit from Cerius
228. ences is any of col index col name column index column name name The column name Setting display formats must be enclosed in quotes if it contains spaces You can refer to rows only within statistical operators Statistical operators The syntax for row cross references is any of row index row name The row name Setting display formats must be enclosed in quotes if it contains spaces Cerius Modeling Environment April 1999 343 11 Working with Tables groups cells and other tables Calculations on models Unary model operators You can refer to groups Grouping table information only within sta tistical operators Statistical operators The syntax for group cross references is group name The group name Creating a named group must be enclosed in quotes if it contains spaces You can refer to a named cell in any expression The syntax for cell cross references is cell name You cannot name cells but some application modules may name certain cells The cell name must be enclosed in quotes if it con tains spaces You can refer to named columns rows groups or cells that are contained in other tables The syntax for table cross references is any of col table_name col_name row table_name row_name group table_name group_name cell table_name cell_nam The table_name is the name of the table in which the named entry is found All names that contain spa
229. enever you start Cerius To set up different lists of active and displayed control panels for use when you run Cerius for different purposes or projects sim ply create separate directories and copy the MSIguirc subdirec tory and its contents to the new directory Then change the panels file as described in Saving control panel configuration If Cerius does not find an MSIguirc subdirectory in the directory in which you start it it looks for an MSIguirc subdirectory in your home directory Please see the on screen help for details on the functioning of each control in the Panel Manager control panel Additional ways of setting Cerius preferences and or performing certain functions automatically are covered under Working with Cerius2 sessions and Controlling Cerius2 from scripts Interface look and feel Finding information Visualizer customization options enable you to change part of the look and feel of the Cerius interface to suit your preferences This section includes information on Interface colors Miscellaneous environment customizations Interface colors Related information Cerius enables you to customize the colors used in the graphical user interface GUI These customizations affect all control panels and all controls within them Color coding of controls according to their function remains consistent Please see Enhancing Model Display for customization of colors used for objects
230. ent Please see the on screen help for details on the functioning of each control in the Bond Calculation Preferences control panel To specify whether Cerius should determine the bond types auto matically by valence satisfaction check the Calculate bond types check box To specify how this algorithm works click the Prefer ences pushbutton next to the Calculate bond types check box in the Edit Connectivity and Bonding control panel to access the Bond Type Calculation Prefs control panel Please see the on screen help for details on the functioning of each control in the Bond Type Calculation Prefs control panel To request bond calculation between all atom pairs that meet the criteria click the CALCULATE pushbutton in the Edit Connectiv ity and Bonding control panel Bonds are added or deleted so that they meet the criteria Subsequent use of the cleaning function 182 Ceru Modeling Environment April 1999 Advanced building and editing Refining the conformation also uses the radii set with the Bond Cal culation Preferences or Edit Elements control panel Hydrogen bonds All or selected hydrogen bonds can be edited and deleted Hydro gen bonds can also be calculated for all or selected atoms based on distance and angle criteria Hydrogen bond criteria When Cerius decides which atom pairs to join by hydrogen bonds it uses these criteria Figure 1 The distance between a potential acceptor atom and a hydro g
231. ent menu item to access the Orient View control panel Click the CENTER pushbutton Any nondefault definition of the center of rotation is cancelled by such actions as resetting the view Resetting the view or filling the window Filling the model window Please see the on screen help for details on the functioning of each control mentioned here Mouse functions and keyboard shortcuts are summarized in Mouse and Keyboard Actions Moving models relative to one another You can move one model relative to another for example to inves tigate how a ligand fits in a receptor site Although the models technically occupy separate model spaces this functionality allows the models to behave as if they have been Cerius Modeling Environment April 1999 237 8 Viewing and Displaying Models Accessing the tools Bringing two models into one conjoined space Specifying the current model Translating the current model Specifying the translation axis Rotating the current model redefined as submodels constituting one model in one model space Select the Move Model Move menu item to access the Model Space Transforms dcontrol panel The current model is the one that is rotated and or translated Alternatively you can use mouse keyboard combinations to con trol movement of the current model Simply make the desired models visible Controlling model visibility and the display mode Using the overlay display mode C
232. ent April 1999 229 8 Viewing and Displaying Models Table 6 Finding information about viewing models If you want to know about Centering orresetting the model display Screen coordinates Zclipping Kekule or resonant display of phenyl rings Space filling models Structural display of charged inorganic systems Thermal motion of atoms Adding lines boxes circles etc to display Labeling models with geometric measurements Viewing close contacts Controlling colors used in displaying models Changing the display and print resolution Other advanced control of model rendering and lighting Displaying Connolly surfaces Changing the display of model surfaces You should already know Read Setting position and orientation Figure 3 Window axes in Cerius2 model win dow Cross sections of models Bond order display Atoms as balls Cations as polyheara Thermal ellipsoids Custom annotations Measuring models Calculating close contacts Model display colors Resolution and graphical quality Enhancing Model Display Model surfaces Surfaces style and transparency The basics of starting Cerius and using its interface are demon strated in Introducing Cerius2 and described in The Cerius2 Interface You need to know how to build Basic building and or load Load ing model structure files a model and should know how to select atoms in your model Selecting atoms and groups of atoms
233. entry box Finding model file s Navigate the directory structure and find the desired file s To go to a higher level directory use the directory selector popup The current directory is printed on the popup when it is in its inactive state To return to the directory from which you started Cerius click the small pushbutton next to the directory selector popup To open a directory that s shown in the file selector list box including the parent directory indicated by double click the directory name To display the names of files having the desired format set the File Format popup if necessary For example when the File Format popup is set to MSI msi is listed in the filename text entry box as a filename filter and only filenames that end with msi are shown in the file selector list box You can also use the filename text entry box to specify a file directory or pathname or to set up your own filename filter Valid UNIX wildcards and operators are allowed Cerius Modeling Environment April 1999 197 6 Managing Modelsand Sessions If the list of file and subdirectory names is longer than the file selector list box use the scroll bar on its right to move up and down the list Where to put the loaded To choose the target model space set Model Space to CURRENT model or NEW see Handling multiple models for information on model spaces Note If you load a model from a file into an alrea
234. er modules Cerius Tutorials Several guides illustrating the use of Cerius Forcefield Based Simulations CDiscover and Cerius Simulation Tools Discuss forcefields and orcefield based calculations CDiscover in the Cerius and standalone modes and the Open Force Field Force Field Editor Charges Minimizer Dynamics Simulation and Analysis modules Command Script Guide Shows how to capture and replay a script of Cerius commands and how to enhance your com mand scripts with the features of the Tool Command Language Tcl Cerius Installation and Administration Guide Provides step by step instructions for installing and administering Cerius in your operating environment Typographical conventions Unless otherwise noted in the text Cerius Modeling Environment uses these typographical conventions Terms introduced for the first time are presented in italic type For example Cerius Modeling Environment April1999 3 1 How To Use This Guide Instructions are given to the software via control panels Keywords in the interface are presented in bold type In addi tion slashes are used to separate a menu item from a sub menu item For example Select the View Colors menu item means to click the View menu item drag the cursor down the pulldown menu that appears and release the mouse button over the Colors item Words you type or enter are presented in bold type For exam
235. er properties simultaneously select the Build Edit Atoms menu item This gives access to the Edit Selected Atoms control panel Please see the on screen help for details on the functioning of each control in the Edit Selected Atoms control panel Cerius Modeling Environment April 1999 167 5 Building Models Specifying the bond type Changing the bond type Tip Additional controls over bonding Additional information To change the bond type between any two atoms use the Edit Bond button in the Sketcher control panel Choose SINGLE DOUBLE TRIPLE or RESONANT from the popup to the right of the Edit Bond tool Changing the default bond type automatically activates the Edit Bond tool If the bond type is already correct you can activate the Edit Bond tool by clicking it You can change bonds in the model window to the type specified by the bond type popup in several ways Select the Edit Bond tool and then pick two atoms If a bond exists between the atoms it is changed to the type specified If no bond exists one of the desired type is created Select the desired atom pair s Selecting atoms and groups of atoms and then double click the Edit Bond tool Existing bonds are changed to the type specified No new bonds are created if more than two atoms are selected You can also change the bond type while in sketch mode see While in sketch mode you can also If you want to edit the bond type and a
236. ered series of independent coordinates in a plane The data points in a set may be connected by lines or dis played in styles such as histogram points or delta lines A 2D Cartesian data set is a regular grid of points in a plane some times with symmetry properties Each point is associated with a real value such as an intensity or an energy Different real values are usually color coded to differentiate them A 2D polar data set is similar to a 2D Cartesian data set except that it is mapped in polar coordinates 294 Cerius Modeling Environment April 1999 Accessing the tools Specifying the type of graph Additional information Creating graphs A special type of 2D data set is used to display LEED RHEED reflections and single fiber diffraction patterns These are called x y z plots where circles whose radii represent the value of the z coordinate are drawn in the xy plane This is different from a 2D contour plot in the delta style The latter draws circles on a regular grid whereas the x y z plot places circles only as prescribed by the x y coordinates If you already have the Gallery Manager control panel open Accessing the tools click the Graph Manager pushbutton in the Gallery Manager control panel to access the Graph Manager con trol panel Alternatively select the Graph Manager menu item from the GRAPHS card to access the Graph Manager control panel Set the Type popup to the desired graph type P
237. erences The label on a labeled button indicates what action occurs if you click the button Radio buttons are used to select only one of a group of options An action button or run button performs the associated action usually indicated by the label and or some nearby text when you click it Popups and similar controls display a list of options when clicked from which you can select one by dragging the cursor Entry boxes are used to display current values and enter new ones To enter the exponent portion of a double precision number in an entry box that is used for entering numbers use an E followed by a signed number for example enter 1 234e 4 for 0 0001234 and enter 1 234e4 for 12340 0 If you are unsure about the function of a particular control click it with the right mouse button to obtain help see On screen help Clicking the close button in the upper right corner of the control panel border closes the control panel 140 Cerius Modeling Environment April 1999 Controls and control panels Clicking the button in the upper left corner gives access to some of your system s window manager functions Managing control panels Opening control panels To access a control panel you select a menu item from the main Visualizer control panel The menu bar select an item from a card Deck of cards menu or click a pushbutton in an open control panel Instructions for accessing particular control p
238. erences control panels Use the Render Models control panel to specify the model s and atoms that you want to be rendered as well as the rendering method For raytracing you may want to change how shiny or dull the atoms appear and how jagged or fuzzy the image appears by 288 Cerius Modeling Environment April 1999 Additional information Stereo viewing using controls in the Raytrace Preferences control panel You can also use this control panel to specify that the intermediate files be saved and to give them a common root name For PSYCHO you can use the Psycho Preferences and More Psy cho Options control panels to set many available options Click the RENDER pushbutton in the Render Models control panel to start the rendering process Depending on your computing power the rendering process may take some time There may also be a delay before the model reap pears if you move the Cerius2 Ray Tracing window To close the Cerius2 Ray Tracing window click anywhere in it Please see the on screen help for details on the functioning of each control in the Render Models Raytrace Preferences Psycho Pref erences and More Psycho Options control panels Stereo viewing Accessing the tools Specifying stereo display In stereoscopic viewing mode an impression of three dimension ality can be achieved by using an appropriate stereo viewer or if you can manage it by crossing your eyes Select the View Graphic
239. erring to other cells in expressions Refering to models in expressions Displaying atom atom distances and other measurements Displaying vector properties Updating calculations Column width and row height Aligning cell contents Adding and removing rowsand col umns Saving tables to files Saving models with tables What kinds of data are associated with models Formatting ASCII files as tables Mouse buttons and keyboard use Uses of tables Read Table expansion and cursor control Understanding cell values types and formats Understanding cell values types and formats Assigning data types Technical notes Setting display formats Editing cell contents Entering your changes Copying moving and clearing information Selecting rows and columns Entering mathematical expressions Concepis Operators Copying models into columns Cross references Calculations on models Setting up calculations on moa els Measuring models Vector properties Recalculating table values Changing row column and heading sizes Aligning information within columns Inserting and deleting entire rows or columns Table expansion and cursor control Saving a table Saving tables containing models What is saved as a model Importing an ASCII text file into a new table Mouse and Keyboard Actions You can use Cerius tables to deplay and manipulate tabular information generated by Cerius f app
240. es which are purchased sepa rately The animation process Animating a model is a three stage process You first need to select a trajectory trj file and load the information from it Next you build an animation sequence Alternatively check the Automate Build check box before loading the file Finally the model is ani mated by playing back the animation sequence Accessing the tools Select the View Animation menu item on the main control panel s menu bar to access the Animation control panel Loading a trajectory file Use the file browser and selector tools to choose the trajectory file from which to construct the animation sequence How to use these tools is detailed under Loading model structure files All file brows ers work similarly If the trajectory file you request appears to be associated with the current model Cerius asks if you want to use this model as the initial frame of the trajectory Otherwise Cerius loads the associ ated MSI format model file as the current model Building an animation To build an animation sequence that uses all frames from a trajec sequence tory file simply check the Automate Build check box before selecting the trajectory file To use only selected frames from the selected trajectory file click the Frame Filter pushbutton to access the Frame Filter control panel Use this control panel to select a subset of the frames you can specify the starting and ending frame
241. es only to the substitution of aluminum Generally this rule is used in the random replacing of silicon by aluminum in zeolite structures Application of Lowenstein s rule ensures that no two aluminum atoms share a common oxygen This may mean that the target replacement ratio is not met A mes sage in the text window reports the actual ratio that is achieved 184 Cerius Modeling Environment April 1999 Advanced building and editing Nonperiodic and periodic Substitutional disorder can be applied to nonperiodic models and models Tip Performing substitutional disorder Additional information to periodic models without symmetry To apply disorder to symmetric crystal structures first convert the structure to a primitive superlattice as described in the Cerius Builders documentation and then perform substitution To introduce substitutional disorder into a model select the Build Disorder menu item to access the Disorder control panel You can use this control panel to Apply the substitution to the whole model or to selected atoms Specify what element is to be replaced by what element and the target ratio to be achieved For example you can replace all silicon atoms in a model with aluminum by setting the target ratio to 0 or replace one fourth of the silicons with aluminums by setting the ratio to 3 0 Apply Lowenstein s rule if you are replacing silicon with alu minum Please see the on sc
242. ess Management control panel 385 386 387 Projection control panel 257 258 projects organizing files 209 382 392 394 properties color mapping 267 274 Psycho Preferences control panel 288 289 pulldown menu 9 pullright menu 42 R R groups adding 13 radio buttons 140 Range Mapping Color Selection control panel 277 Raytrace Preferences control panel 288 289 ray tracing 287 Record Commands control panel 377 378 reinitializing Cerius2 212 213 380 446 Cerius Modeling Environment April 1999 remote hosts 385 Render Models control panel 288 289 reset function 137 reset tool 25 resetting Cerius2 212 restarting Cerius2 212 resuming work after interruption 213 rings closing 152 phenyl 250 Rotate Atoms control panel 176 run buttons 140 S Save Connolly Surface control panel 225 226 Save Graphs control panel 309 Save Model control panel 210 211 Save Preferences control panel 210 Save Session control panel 213 Save Table control panel 326 327 saving a model 21 scroll bar 15 scrolling 15 select definition 132 example 9 selecting a menu item 9 selecting atoms 25 all atoms 160 beep 152 159 by additional criteria 162 by element 161 by forcefield type 161 by name 161 comprehensive description 158 cumulative 160 deselecting 160 short ends 161 tools 159 selecting chains 161 selecting filenames 198 selecting fragments 161 selecting groups 163 selecting residues 161 selection criteria defined 161 sele
243. f pick target selection criterion and selection scope pick target what is selected selection can be within atom The atom s actually picked1 In one model In all models see Selecting atoms in sev eral models atom All atoms of the same name Allin the same residue All atoms of the same element type Allin the same chain All atoms of the same forcefield type Allin the same model Allin al models atom All atoms in the same fragment In one model Smallest set of bonded atoms In all models residue All atoms in the residue s actually In one model picked In all models residue All atoms in all residues of the same type All in the same chain Allatomsin all residues of the same ID Allin the same model Allin all models chain Allatomsin the chain s actually picked In one model In all models chain Allatomsin all chains of the same name All of this chain name in the same model All of this chain name in all models model Allatomsin the model picked All atomsin all models 1Default value 20rin all visible models orin selected models Selecting groups You can select groups by clicking the Select objects action button in the Groups control panel or the Select Group button in the Atom Selection control panel Customized atom selection You can set up sophisticated and or multiple selection criteria and or obtain even more precise control over what is selected when you pick an atom
244. files see Cerius Command Script Guide Recording commands is discussed under Command logging and scripting Playing back scripts and log files Accessing the tools Finding the script file Playing back Cerius scripts Additional information If you have certain tasks that you nearly always perform during a Cerius session you can record them in a command script file and then have Cerius automatically perform these tasks from the script either immediately Starting Cerius2 with a command script file or when you request it this section Then you can proceed with additional tasks using the graphical interface Select the Utilities Playback Script menu item in the main Visu alizer control panel to access the Playback Script control panel Use the file browser and selector tools to find and choose the desired script file How to use these tools is detailed under Finding model file s All file browsers work similarly You can play back the script file in several ways To simply run the script now click the RUN pushbutton in the Playback Script control panel To reinitialize the session Starting a new session before running the script check the Re initialize check box and then click the RUN pushbutton Torun the script repeatedly reinitializing the session before each pass through the script check the Run Script Repeatedly check box and then click the RUN pushbutton Please see the on screen hel
245. forcefields to locate pcff Note that references are written to the textport for your Cerius Modeling Environment April 1999 119 3 Tutorials information A molecular mechanics forcefield contains different sets of parameters different bond lengths etc for atoms in different bonding environ ments For example the oxygen in a carbonyl group will be modeled using different parameters than those used for oxygen in an ether group or in water carbon in benzene will be given different parameters to car bon in ethanol or in ethene Before running the simulation it is neces sary to identify these different atom types 2 Identify the atom types Open the Atom Typing menu by holding down the Typing option on the OPEN FORCEFIELD card and selecting Atoms Select the Run button next to Calculate using typing rules to ask Cerius to identify the atoms types for all the atoms in the current model the glucose molecule Change the Atom Labeling popup on the tool bar from NO LABEL to FFTYPE and then to CHARGES Note that the oxygen atoms and carbon atoms in different bonding envi ronments have been identified as different atom types Once the atom types and bonding environment were identified partial charges were automatically allocated to each atom 3 Minimize the energy of the model Select the MINIMIZER card from the OFF METHODS card deck it is usually the first card in this deck During mol
246. formation Additional information Interface look and feel Please see the Installation and Administration Guide for additional information To enable or disable display of small explanatory boxes whenever the cursor lingers over certain controls for example many of the tools in the Visualizer s main control panel check or uncheck the Activate balloon help check box in the Customize Environment control panel You can adjust the pitch and volume of the beeper bell with the Tone and Volume controls respectively in the Customize Envi ronment control panel You can choose to have brief information on atom properties sent to the text window whenever you click an atom To do this check the Echo object reference on pick check box in the Customize Environment control panel Uncheck the box to turn this feature off Please see the on screen help for details on the functioning of each control in the Customize Environment control panel Cerius Modeling Environment April 1999 397 14 Customizing the Interface 398 Cerius Modeling Environment April 1999 References Atomic Coordinate and Bibliographic Entry Format Description Pro tein Data Bank January 1985 Connolly M L Science 221 709 1983 Connolly M L J Appl Crystal 16 548 1983 DBWS9006 Manual 14 1991 ICSD User Manual Fachinformationszentrum FIZ Karlsruhe 59 1991 MolEN Manual Enraf Nonius 1 154 1990 Neider J Dav
247. g bonds and ellipsoid axes Size of ellipsoids Other atoms non cations can be represented as crosses small spheres or single pixels or not drawn at all To change how other atoms are displayed click the Preferences button in the Display Attributes control panel to access the Style Preferences control panel Then set Non Polyhedral Style to CROSS BALL POINT or NONE Ellipsoid style represents a constant probability surface for the thermal motion of the atoms Atoms described by anisotropic tem perature factors are represented by ellipsoids Atoms described by isotropic temperature factors are represented by spheres Lines representing bonds are drawn by default but can be removed The orientation of the ellipsoid s principal axis may be displayed Spheres and ellipsoids are drawn only if the temperature factors describe a solid object In mathematical terms the matrix must be positive definite If this is not true or if no temperature factor has been specified atoms are represented by crosses To display atoms as thermal ellipsoids you must first be sure that anisotropic temperature factors see Understanding the display and Temperature factors have been specified or loaded Then you can Set the display style popup on the toolbar to ELLIPSOID or Select the View Display Attributes menu item to access the Display Attributes control panel Set the Style popup to ELLIP SOID To show or hide the principal el
248. g cyclohexane and saving the structure to file In the following steps you open the Sketcher panel and use its Sketch H Adjust and Clean tools to build a model of cyclohexane After you build cyclohexane you save it into a structure file 64 Cerius Modeling Environment April 1999 Using the 3D Sketcher 1 Start Cerius and open the Sketcher If Cerius isn t already open type gt cerius2 in a UNIX shell to run the program The program takes a few seconds to initialize a welcome screen appears briefly at first and then the Cerius GUI appears Open the Sketcher control panel by selecting the Build 3D Sketcher item The Sketcher control panel appears 2 Sketch the cyclohexane model Choose the Sketch icon e Note the Sketch With element is set to C for carbon Notice also that in the model window the mouse cursor appears as an inverted V this indi cates that the mouse is now in sketching mode Click once in the model window A single carbon atom appears represented as a cross and a dotted guideline follows the mouse cursor Keep the cursor within the model window if the cursor moves out of the model window you lose the guideline Cerius Modeling Environment April1999 65 3 Tutorials Troubleshooting If you lose the guideline click once on the first carbon atom with the mouse still acting in Sketch mode and the g
249. g number is the attribute s value A C Label H1 3 Atom A I ACL 6 c A F Charge 0 11 A D XYZ 1 087 0 0 D double precision type attribute the three values are an array A C Label C2 4 Atom A I ACL 1 H A F Charge 0 028 A D XYZ 1 4493 1 02483 0 A C Label H3 A I ACL A D XYZ 1 H 1 44936 0 51245 0 88749 A F Charge 0 028 A C Label H4 6 Atom A I ACL 1 H A F Charge 0 028 Cerus Modeling Environment Apnrl 1999 417 D File Formats A D XYZ 1 44934 0 51236 0 88756 A C Label H5 7 Bond Bond is the object type and delimits data for first bond A O Atom1 2 O object OD type attribute A O Atom2 3 8 Bond A O Atoml 3 A O Atom2 4 9 Bond A O Atoml 3 A O Atom2 5 10 Bond A O Atoml 3 A O Atom2 6 Allowable attribute types are B byte C string D double preci sion number F floating point number I integer O object ID S short T table Allowable object types include ACL Atom Bond Group SCL Sequence Subunit string Allowable values are scalars number or quoted string arrays values in parentheses separated by white space tabular data MSF The Molecular Simulations File MSF format enables you to com municate with the QUANTA CHARMm software MSF files default extension msf store element types coordinates connec
250. g the column s in that order Those column names or numbers automatically appear in the correct entry boxes in the Sort Table control panel You cannot use columns containing model data Models in tables as sort criteria unless the column contents are displayed as object IDs However you can use a binary Binary model operators or unary Unary model operators model operator in an expression in some other column and use that column as a sort criterion Specify whether the sort order for each criterion is to be Ascending or Descending by setting the popups under each of the criterion entry boxes You can specify whether all or only part of the table is sorted To sort the entire table select the All Rows control To sort only selected rows select the Selected Rows control You usually have to specify search criteria from the Sort First 362 Cerius Modeling Environment April 1999 Starting the sort Additional information Graphing table information By and Then By popups instead of by selecting columns if you use this option To sort only rows contained within a group if any exist in the table see Grouping table information select the Group control and specify the group by choosing its name from the associated popup All nonsorted rows remain in their original positions within the table When you have specified all your desired options click the SORT pushbutton to initiate the sort Please see the on scre
251. ge your mind If a process is running when you stow the main control panel to a desktop icon see Managing control panels the Cerius icon dis plays a progress meter Other windows containing controls and or static or dynamic information appear as needed Some examples and where you can find more information on them are Graph window Working with Graphs Table window Working with Tables Rendering windows Rendering and ray tracing Periodic table window Building Models e g Dummy atoms 144 Cerius Modeling Environment April 1999 This section explains Building Models The Cerius e Visualizer provides a variety of tools for making new models and changing existing models These include a mouse driven 3D Sketcher for constructing and editing models this sec tion as well as features that enable you to position atoms pre cisely Precise positioning of atoms during building edit the properties of selected atoms or elements Editing element and bond attributes change bonding Changing the hybridization and adjusting the valence and introduce disorder Introducing substitutional disor der You can also annotate the model by adding items such as text arrows and boxes Viewing and Displaying Models These general purpose basic and advanced building and editing tools are directly available from the Build Edit and Move pull down menus on the main control panel s menu bar Other builde
252. gement control panel Executing Cerius on one machine while displaying its interface on another is discussed in the Cerius Installation and Administra tion Guide Cerius Modeling Environment April 1999 387 13 Scripts and Licensing 388 Cerius Modeling Environment April 1999 Customizing the Interface You may want to rearrange the Cerius decks of cards specify that certain control panels be open or easily accessible when Cerius starts change the interface colors or set various other environ ment customization options This section explains This section contains information on Interface configuration Interface look and feel Table 26 Finding information about customizing Cerius2 If you want to know about Read Creating and adding cardsto card decks Deck of cards menu configuration Using configuration files How it works Displaying closing reorganizing control pan Control panel management elson the screen Starting C erius with open control panels Control panel management Customizing Cerius control colors Interface colors Launching Cerius from the desktop Cerius2 as a desktop icon Pitch and volume of the bell Adjusting the beeper Customizing coloruse in the model and Model display colors Customizing display colors graph display windows Customizing Cerius by meansof command Starting Cerius2 with a command script file scripts Customizing C erius by means of session pref
253. green and blue To return to a neutral colored ambient light click or adjust the Gray control 282 Cerius Modeling Environment April 1999 Lighting control Defining disc rete light sources Preliminary activities Finding information Colorand components Accessing the tools Brightness and color of ambient diffuse and specular components You can illuminate your model with one or more discrete light sources to spotlight various features and to dramatize its appear ance First choose which light source to define or redefine from the Light popup on the Lighting control panel see Accessing the tools and check the Enabled check box to turn it on Turn off other lights see Tip if you want to see the effects of only the light you are defining This section includes information on Color and components Directional lights Positional lights Spotlights Light attenuation Adjusting the ambient diffuse and specular components of a light source affects the perceived color of an object and makes it appear shiny or matte Concepts Click the Color pushbutton on the Lighting control panel to access the Lightsource Colors control panel To change the brightness of the Ambient Diffuse and Specular components of your light source adjust the appropriate Gray con trol in the Lightsource Colors control panel To adjust the colors of the Ambient Diffuse and Specular com ponents of your light source use th
254. h with tool Cerius Modeling Environment April1999 151 5 Building Models Adding atoms and single bonds Placing the first atom Tip What next Tip To begin sketching simply click the Sketch with tool to activate it if it is not already active when an icon type tool is active it is colored dark purple When you move the cursor into the model window it is shaped like a triangle indicating that you are in sketch mode that is that clicking the left mouse button places an atom and or bond rather than selecting an atom or some other activity The element that is used in sketching is specified as described under Selecting the element type You can use the Sketch with tool to start building a new model and to add atoms to existing models Click anywhere in the model window to place the first atom Move the cursor away a dashed line follows the cursor connecting it with the atom you clicked and indicating where the bond to your next atom will lie If you already have one or more models loaded into or built during your current Cerius session you need to create a new empty model space in order to start building a new model please see Creating clearing and deleting model spaces After placing the first atom or when adding to an existing model you can use the sketch mode for several tasks To place a second atom click where you want it to appear Con tinue clicking to place subsequent atoms in a c
255. h data sets to display and edit for editing are discussed above Specifying immediate or delayed updates of the graph dis play is presented under Selecting graphs to display You can also edit the color ranges see Color ranges that are used to color code values shown in graphs Select the Data Plotting Attributes menu item from the GRAPHS card to access the Plotting Attributes control panel Alternatively click the Plotting Attributes pushbutton in the Graph Manager control panel to access the Plotting Attributes control panel The controls available in this control panel depend on the type of graph you have selected for editing To change the plot style used for selected data sets in x y graphs set the Style popup To change the line style when the plot style is line histogram or delta used to plot selected data sets in x y graphs set the Lines popup Styles other than SOLID work best when data points are spaced relatively far apart To change the color used for selected data sets in x y graphs select a color from the Color popup To change the style contour lines continuous shading or delta used to differentiate ranges of values in 2D Cartesian and 2D polar graphs set the Style popup For 2D Cartesian and 2D polar graphs as well as x y z graphs you can specify The color range Color ranges that is used The direction in which the color range is used for the contour and continuous styles of 2D graphs th
256. h window although the previous graphs and their data sets are still present in memory However you can load a graph file without display ing its graph s immediately Select the Gallery Expert Functions menu item from the GRAPHS card to access the Graphs Expert Functions control panel Alternatively click the Expert Functions pushbutton in Cerius Modeling Environment April 1999 307 10 Working with Graphs the Gallery Manager control panel to access the Graphs Expert Functions control panel Preventing old graphs After the first graph is output from an application module set the from being overwritten Data Placement popup in the Graphs Expert Functions control panel to ADDITIONAL GRAPH When a new graph is generated by your application module both it and the older graph are displayed in the graph window Adding new data toan After the first graph is output from an application module set the existing graph Data Placement popup in the Graphs Expert Functions control panel to COMBINE WITH EXISTING When a new graph is generated by your application module the new data set is displayed in the older graph that is already dis played in the graph window Additional information Please see the on screen help for details on the functioning of each control in the Graphs Expert Functions control panel Removing graphs and data from a Cerius session You can remove all graphs and their data sets from the graph win dow and
257. hain To end a chain double click when you place the last atom click again on the last atom added or move the cursor outside the model window The dashed line no longer appears When you click an atom Cerius beeps to indicate that you succeeded To close a ring or connect a chain to an existing ring or chain click the appropriate existing atom 152 Cerius Modeling Environment April 1999 Tip Other sketch mode func tionality Precise positioning of atoms during building Basic building To place a bond between two atoms that are not bonded to each other click each atom You can also use the Connect tool or the Edit Bond tool for this purpose see Connecting fragments and Changing the bond type To start a new chain or ring end the first one see above and then click in empty space To adda branch to an existing chain or ring click the atom that is to be the branch point then click in empty space To sketch with a different element type select a different ele ment type Selecting the element type then click the atom in the model window to which you want to add the new element You do not need to specifically add hydrogen atoms this can be done automatically while sketching or more quickly after sketching is completed Adding hydrogens While in sketch mode you can also Change the type of bond from single to double or from double to triple by clicking the atoms at each
258. he Lighting control panel to LIGHT 2 and checking i e clicking so that a checkmark appears in the check box the Enabled check box 44 Cerius Modeling Environment April 1999 Exploring Cerius on yourown Use the Lightsource Colors control panel to change the color of LIGHT 2 Make it different from LIGHT 1 so you can more eas ily see what s happening as you adjust the lights 37 Changing the model window s background color Select the Utilities Customize Pen Colors menu item In the Pen Colors control panel set the Background popup to OTHER or set the Pen popup to BACKGROUND Use the color sliders to customize your background s color Or just set the Background popup to one of the predefined color choices Exploring Cerius on your own 38 Using the Help menu Select the Help Getting Started menu item You can use the buttons in the Getting Started control panel to find out more about The names of the parts of Cerius s graphical environment and how to manage all the windows Loading models Manipulating models in the model window including Access to on screen summaries of mouse and keyboard actions for selecting and moving models Information on changing the display style and atom colors as well as on labeling atoms Cerius Modeling Environment April1999 45 2 Introducing Cerius Building models icons in some of these help panels function
259. he H Adjust and Clean buttons Highlight the Selec tion mode icon once mote Rotate and view the model try some other display styles then return to the Stick display Choose the Twist icon In the model window the mouse cursor for twist mode is shaped like a bow tie 72 Cerius Modeling Environment April 1999 Using the 3D Sketcher You must select four atoms to define a twist torsion Pick the hydrogen attached to the oxygen the oxygen itself the carbon attached to the oxygen and one of the adjoining ring carbons In this case don t hold the lt Shift gt key down the atoms don t become highlighted when they are selected in Twist mode Drag the mouse over the model window with the left mouse button depressed to increase decrease the torsion The change in the torsion angle is interactively updated Note that the atom picked last is the one that moves 2 Try the other geometry manipulation tools Use the Stretch and Angle tools which work similarly to Twist 3 Save the new structure Save the phenol structure into a file called phenol msi If necessary see Step 6 on page 68 for a reminder of how to save Clear the model window Cerius Modeling Environment April1999 73 3 Tutorials E Building xylene from template fragments In the following steps you use the template tool to create a model of p xylene The template tools let y
260. he Utilities Customize Color Mappings menu item from the main Visualizer control panel to access the Edit Color Mappings control panel Alternatively if you have the Color Selected Objects control panel open Accessing the tools you can click its Edit Mappings pushbutton to access the Edit Color Mappings control panel Type a name in the New Map entry box Enter it by pressing lt Enter gt on the keyboard or clicking elsewhere in the control panel Identify what type of property is to be mapped by choosing an item from the Attribute popup in the Edit Color Mappings control panel Specify that the property to be mapped will use just two on off colors by setting the Type popup to BINARY The contents of the bottom of the Edit Color Mappings control panel depend on the value of the Type popup Set the color popups to the desired colors for the on and off values You can also choose to color only the on or off value by setting the other to Use As is To apply the map to your model select the desired atoms and choose your new map s name in the Color by a Property list in the Color Selected Objects control panel Coloring atoms according to a property If the map is already applied to your model any changes you make to the on and off colors appears immediately in the dis played model If you want some color that s not available in the popups click the More On Colors or More Off Colors pu
261. he model window to place the tail of the arrow Without releasing the mouse button drag the arrow out by moving the cursor then release the mouse button to place the head of the arrow The new arrow uses the currently set annotation color and line width see Editing the annotation objects To add rectangles or squares to the model display you use the Rectangle tool Check the Filled check box if you want a filled rectangle assure that it is unchecked if you want an outline rectangle Cerius Modeling Environment April 1999 245 8 Viewing and Displaying Models Editing the annotation objects Select the Rectangle tool then click the left mouse button in the model window to place one corner of the rectangle Drag the rect angle out by moving the cursor then release the mouse button to place the opposite corner of the rectangle The new rectangle uses the currently set annotation color and line width see Editing the annotation objects For filled rectangles the fill color is the same as the outline color To add circles to the model display you use the Circle tool Check the Filled check box if you want a filled circle assure that it is unchecked if you want an outline circle Select the Circle tool then click the left mouse button in the model window to place the center of the circle Drag the circle out by moving the cursor then release the mouse button to place the cir cle The new circle uses the currently
262. he table manager tool bar or Select the File Revert menu item from the TABLES card 318 Cerius Modeling Environment April 1999 Additional information File formats Managing and editing tables Any changes you made since you last saved the table are lost when the table file is reloaded Please see the on screen help for details on the functioning of each control in the Open Table control panel Note that two different filetypes end in tbl those produced by Cerius are table files but those produced by Insight II are graphs Importing an ASCII text file into a new table File format Accessing the tools Finding the file You can create a table by importing appropriately formatted data from an ASCII text file To be imported into the Cerius Tables module the file must be as ASCII text file and meet these requirements Columns of numerical or text data must be separated by a spe cific separator character The same character must separate each column Ifacolumn contains text and at least one entry in that column consists of more than one word each entry in the text column must be enclosed in a specific delimiter character For example Sample x1 x2 X3 x4 A 17 7 26 6 60 B 16 12 9 15 52 GM 11 56 8 20 D 118 11 31 8 47 A 12 7 52 6 33 To access the Import Table control panel Click the IMPORT tool in the table manager tool bar or Select the File Import menu item from
263. he thin blue lines disappear D Manipulating contol panels In the following steps you learn about control panels how to open close scale and stack them You use on line help to get information about the controls on the panels And finally you learn how to re ini tialize and or exit from Cerius 1 Close and open control panels Close the Load Model control panel by clicking on the close box pl in the right corner Cerius Modeling Environment April1999 57 3 Tutorials All control panels can be closed this way Open the Save Model control panel by choosing File Save Model Notice that those pulldown menu items that open control panels all have names that end in ellipses 2 Open more control panels Choose Build Element Defaults to open the Edit Elements control panel You would use the Edit Elements control panel if you wanted to alter any element properties such as the display color used in Cerius Choose View Display Attributes to open the Display Attributes control panel The Display Attributes control panel has the same functionality as the Display Style and Atom Labeling tool bar popups which you have already used You can select the Preferences button to change the defaults for the dif ferent displays For example you can change the size of the spheres in the Ball display from 0 7 to 1 0 in van der Waals radii of the atoms 3 Access help for a co
264. he valence For setting the hydrogen bond angle criterion please see Hydrogen bonds Examining and changing torsions Important Changing a torsion manu ally Cleaning a structure Refining the conformation automatically optimizes all torsion angles You can change torsions before cleaning if you want to bias the final structure However if you want a different specific torsion angle than that determined automatically change it after using the clean function clean only selected atoms Control of the model cleaning function or do not use cleaning To change a torsion angle manually select the Twist tool in the Sketcher control panel Then click either two or four contiguous bonded atoms Click two bonded atoms and then click the second atom again to define the Cerius Modeling Environment April 1999 173 5 Building Models Precise change in torsions Additional information Default torsions bond that you want to twist Click four atoms to define the specific torsion angle to be changed The torsion angle in degrees is displayed next to the torsion in the model window when you click in empty space To change the torsion angle click and drag the cursor in empty space in the model window Dragging up and or to the right increases the angle dragging down and or to the left decreases it Torsions in rings cannot be changed You can also modify torsions by rotating parts of models manually Rotating atoms manua
265. hen it s in the model window 20 Cerius Modeling Environment April 1999 Saving a model Saving a model 11 Saving your caffeine model Now that you ve built a model you can save it Select the File Save Model menu item The Save Model control panel appears If you named your working directory CeriusIntro as suggested in Step 1 and did not save any other files in this directory the Save Model control panel should look like this O Save format F Cerius2 Models Cerius2 Resources Click in the text entry box next to the SAVE button Change msi to caffeine msi and click the SAVE button Cerius Modeling Environment April1999 21 2 Introducing C erius If you neglect to type the msi Cerius adds it automatically The msi helps you remember that the file is in Cerius s standard for mat 12 Cleaning up your screen By now you have several control panels scattered about your screen You can close one control panel Closing control panels Click the close button qj in the top right corner of any control panel Or you can close all open control panels at once Click the clear panels tool Bl on the toolbar of the Visual izer main panel The toolbar is just below the menu bar and looks like By now you might want to relax and have a cup of real caffeine 13 Interrupting this tutorial optional If you need to quit your Cerius ses
266. how to use the Visualizer Another guide Cerius Builders describes the specialized builder modules you can add to the Visualizer to supplement its basic model sketching capabilities Each other optional application module or group of related modules includes its own documenta tion Cerius Modeling Environment April 1999 127 4 The Cerius Interface Starting C erius Example Cerius is started by invoking the cerius2 script which is typically located in msi cerius2 runtools On your system the script may have been copied or linked to a standard directory in your search path such as usr local bin If not you may want to set up and use an alias If you are not sure how your system is configured please ask your system administrator Once you are correctly set up you should make a working direc tory in which to run Cerius You should have write access to such directories Write access is necessary because symbolic links and log files are created in the startup run directory during a Cerius session You may want to create subdirectories in which to store related Cerius files for each of your projects and use one of these as your run directory Start a regular Cerius session by changing cd to the desired run directory and entering at the UNIX prompt gt cerius2 A specific example of starting Cerius is presented under Starting Cerius2 Initial layout of the Cerius screen The key GUI elements
267. ight in the Row Height entry box and click the APPLY TO pushbutton Rows may not be less than 0 25 inches high If more than one row or column is selected all are resized equally To change the depth of column headings access the Table Proper ties control panel as above see Accessing the tools and set the Prop erties popup to Heading Enter the desired value in the Column Heading Height entry box and click the APPLY TO pushbutton Column heading rows may not be less than 0 25 inches high To change the width of row headings access the Table Properties control panel as above see Accessing the tools and set the Proper ties popup to Heading Enter the desired value in the Row Head ing Width entry box and click the APPLY TO pushbutton To change how cells are delineated access the Table Properties control panel as above see Accessing the tools and set the Proper ties popup to Grid Set the Horizontal Lines and Vertical Lines as desired and click the APPLY TO pushbutton Please see the on screen help for details on the functioning of each control in the Table Properties control panel Values and mathematical expressions Finding information A mathematical expression can be applied to a cell or column The cell displays the value derived from the expression not the expres sion itself The expression may contain scientific constants binary math and text operators built in operators unary math and text operators trigono
268. iles version numberof software in which file format waslast changed for example 300 for version 3 0 of POLYGRAF DESC RP 1X A8 Descriptor DESCRP a short descriptor for the file Can con tain upper lower casesand spaces REMARK 1X A File Description REMARK descriptive information about the file FO RC EFIELD ASCII force field name FORCEFIELD name of the force field 1X A8 5 PERIOD per PERIOD 1X 3I1 Periodicity in x y and z PERIOD O 1 O 1 0 1 flagsindicate odic files only 6 AXES per odic files only AXES 3X A whether periodic in x y and 2 Ignored on reading set to 111 when writing crystals Axisorder AXES orderof axes forexample zyx Ignored on reading set to zyx when wnting crystals Cerius Modeling Environment April 1999 419 D File Formats Record 7 SGNAME periodic files only 8 CRYSIX peri C RYSTX 1X odic files only 9 CELLS peri odic files only Format Storage SG NAME 1X Space group information SGNAME space group name A8 1X A8 215 Scho nflies symbol forthe space group space group number case number A case numberis only used forspace groups where there isa choice of unique axis cell origin oraxis geometry Note Ignored on reading because all atoms including sym metry copies are contained in atom records Cell parameters CRYSIX Specification of unit c
269. in To enter a comment in the current RUN LOG file and the current segment log file if one is open enter the desired text into the Enter Comment into Log File entry box To empty and restart the current RUN LOG file from the current point in your Cerius session click the Empty Log File contents Cerius Modeling Environment April 1999 377 13 Scripts and Licensing Additional information action button in the Record Commands control panel This action does not reinitialize the Cerius session Starting a new session it merely restarts the log file Please see the on screen help for details on the functioning of each control in the Record Commands control panel Command tracing Levels of commands Accessing the tools What level of commands to trace Tip Command tracing enables you to view and store various levels of Cerius command output You can also display the commands in the text window as they are generated This output can be useful for monitoring the commands generated during a Cerius session especially if you are logging commands for use in a script Three levels of commands are generated by the graphical interface and application modules Primary Generated by primary command generators such as the graphical interface or a script file or by your direct entry of commands in the text window Secondary Generated directly or indirectly by application modules as a result of processing a
270. in a large square display area with the others in smaller square display areas 32 Adding and deleting model spaces You ve already learned in Step 25 how to add a new empty model space by clicking the tool You can also clear an existing model space i e remove the model leaving its model space empty or delete a model space i e remove both the model and its space from the current 2 Cerius session To delete a model space click a diamond to make the desired model current then click the tool Click OK in the con firmation window that appears The number of models listed in the table decreases by one the remain ing models are not renumbered To clear a model space click a diamond to make the desired model current then click the clear tool Click OK in the confirmation window that appears The model space and the current display area are cleared but the Cerius Modeling Environment April 1999 39 2 Introducing C erius model name and number remain in the model table You may sketch a new model in this display area and model space You may also copy one of the other models into the cleared space if you say wanted to make an analog of caffeine 33 Copying models from one model space to another Leave the cleared model space defined as current the largest display area is empty Click in an empty part of one of the other display areas con tinue holding d
271. in the Cleaner Controls control panel Other builders Tools designed to build more specialized models are available as separate modules and are accessed with the deck of cards menu These include the Analog Builder Crystal Builder Surface Builder Interface Builder Polymer Builder and Amorphous Builder These modules are described in Cerius Builders With these builders you can readily build series of analogous structures crystals and other periodic structures surfaces inter faces polymers and amorphous structures Not all the Sketcher control panel functionality works with peri odic systems Those functions that do work include sketching bonds changing the element hybridization or bond type editing bond lengths angles and torsions and deleting atoms or bonds Cerius Modeling Environment April 1999 191 5 Building Models 192 Cerius Modeling Environment April 1999 Other builders Cerius Modeling Environment April 1999 193 5 Building Models 194 Cerius Modeling Environment April 1999 Managing Models and Sessions Among the many functions that you use the Visualizer to perform are management of the Cerius session and of the models with which you work This section explains This section tells you how to load and save structure files and how to manage Cerius models and sessions Loading model structure files Handling multiple models Saving model structure files Working
272. indow To enter your changes do one of Press lt Enter gt or lt Tab gt on the keyboard lt Enter gt makes the next cell in the column current lt Tab gt makes the next cell in the row current Cerius Modeling Environment April 1999 321 11 Working with Tables Cancelling an edit Additional information Click another cell to make it current To cancel an edit press lt Esc gt on the keyboard The previously entered value if any is restored Mouse functions and keyboard shortcuts are summarized in Mouse and Keyboard Actions Copying moving and clearing information Selecting rows and col umns Copying one or more cells You can copy or move values from one cell row or column to another You can also clear the contents of the current cell or of selected row s or column s without removing the emptied cell s from the table To work with cells columns and rows you generally need to select them first You explicitly select and highlight a row or column by clicking a row or column heading for illustration see Accessing the tools For some purposes implicit selection of a row or column is sufficient the row and column containing the current cell see Selecting a cell are implicitly selected To select a continuous range of rows or columns click the first row or column heading then lt Shift gt click the last row or column head ing in the range lt Shift gt click to select addit
273. indow move the cursor over the control or menu item and click the right mouse button A window containing the requested help text appears in the center of the screen Click the help window to close it or click the right mouse button over another item to obtain more help If you allow the cursor to rest over many controls a small balloon help message appears identifying the tool s function General information about Cerius and basic GUI operations is available from the Help pulldown menu on the main control panel s menu bar An example of using the Cerius help facility is presented in Accessing on screen help Menu card searching The menu card search tool on the main control panel s toolbar gives access the Menu Card Search control panel You can use this control panel to search for a keyword used anywhere in the menu card deck hierarchy or in menu items accessed via the menu bar The search is case insensitive and wildcards can be used For details see the on screen help associated with the controls in this control panel Messages and status information Warnings When you request that Cerius perform some procedure with potentially important consequences e g loss of data a warning message window appears These windows typically give you a chance to confirm or cancel your request or to make an alternative request by clicking a push button control 142 Cerius Modeling Environment April 1999 Time consu
274. ing that the atom has been changed to carbon Change the Edit Element type to O by choosing O from the associated popup or by entering O in the Edit Element text entry box Click the top H on the 6 membered ring Red indicates an oxygen atom Now click the bottom left hydrogen that s directly attached to the 6 membered ring Change the Edit Element type to N Click each of the two carbons in the 6 membered ring to which the methyl groups are attached Remember the methyl group at the bottom of the 6 membered ring does not yet look like a methyl group 8 Correcting the bond order In the Sketcher control panel find and click the Edit Bond tool The Edit Bond tool looks like Cerius Modeling Environment April1999 17 2 Introducing C erius The Edit Bond popup is already set to SINGLE Click one of the nitrogens in the 6 membered ring Next click the carbon at the other end of the double bond that emanates from that nitrogen The double bond becomes a single bond Click the other nitrogen in the 6 membered ring and then the carbon at the other end of its double bond Now change the Edit Bond popup from SINGLE to DOU BLE Click the bottom N in the 5 membered ring and the right most carbon in the same ring Click one oxygen and the carbon to which it is attached Do the same for the other oxygen Your model should now look approxim
275. ing Environment April 1999 259 8 Viewing and Displaying Models You should already know Accessing the tools Specifying what and how to print Additional controls Vector or raster format for printing model windows You need to know what UNIX print command including com mand line options is usually used at your site for sending Post Script output from applications to a printer Please ask an experienced user at your site or your system administrator if you do not know the command Select the File Print menu item to access the Print control panel This contains the primary PostScript output controls and provides access to the Page Setup control panel which contains supplemen tary controls Select the image source by setting Image Capture to Model Win dow or Graph Window The size of the model window affects the image s detail when it is output as bitmap PostScript the larger the window the greater the detail However the size of the graph win dow does not affect the output detail Specify how you want the image to appear by setting Color to Full Color Grayscale or Black amp White Of course your printer must be able to handle the selected color mapping Tell Cerius to send the output to a printer or a file by choosing the relevant PostScript Destination radio button You can enter a file name in the entry box to the right of the FILE button Specify the UNIX print command including pathname if need
276. ing and formation will not be observed using molecular mechanics but could be stud Cerius Modeling Environment April 1999 125 3 Tutorials ied using quantum mechanics models for example using Fast Structure 126 Cerius Modeling Environment April 1999 This section explains Related information The Cerius2 Interface The Cerius product line is a range of molecular modeling soft ware all based on the core control and presentation platform called the Cerius Visualizer The Visualizer is an integrated collec tion of tools whose functions include Cerius session manage ment session logging building and visualizing atomistic models model management saving and loading models 3D graphical representation data presentation and environment customiza tion The Visualizer supports numerous specialized Cerius application modules These plug into the Visualizer and are all controlled with a consistent mouse driven graphical user interface GUI The GUI provides intuitive control of all functions maintaining a consistent look and feel throughout the Cerius environment This section tells you how to run Cerius and introduces basic fea tures of the graphical interface It includes Starting Cerius2 Initial layout of the Cerius2 screen Using the mouse the basics Using the main control panel Controls and control panels Information sources Other windows The rest of this guide describes in detail
277. ing software Brookhaven PDB files default file extension pdb store Cartesian coordinates and element types of atoms Bonding connectivity and crystal unit cell parameters can also optionally be stored although crystal cells are not automatically reconstructed upon reloading into Cerius PDB files consist of 80 character records each with a left justified keyword of as many as six characters that indicates its record for mat type Records can be in any order with at least one ATOM record present Of the many PDB record types in the complete specification only the following are supported in Cerius ATOM CRYSTI1 HETATM 426 Cerius Modeling Environment April 1999 Loading and saving temperature factors in structure files CONECT END Others are ignored on input and blank on output For a full description of the PDB format refer to Atomic Coordinate and Bibliographic Entry Format Description 1985 SHELX The SHELX structure file format default file extension res allows communication with the SHELXTL program the standard for X ray single crystal structure determination It stores element types coordinates connectivity isotropic and anisotropic temperature factors occupancies crystal cell parame ters and symmetry Symmetry is written out and read in as Gen eral Positions Loading and saving temperature factors in structure files The MSI SHELX ICSD DBWS and MolEN structure file formats
278. initializing C erius Resuming a Cerius session Saving preferences Copying models to and from other applications Starting a new session Loading a previously saved session Using saved sessions as preferences settings Customizing the C erius interface Customizing the Interface Running Cerius from scripts con Controlling Cerius2 from scripts tained in log files Loading model structure files Why read this section Related information You should already know Loading models This section tells you how to bring one or more models that are stored on disk into your current Cerius session These can be models supplied with Cerius by MSI see Models supplied by MSI or models that you or someone else built and saved earlier Saving individual models Building models is explained in Building Models and demonstrated in Introducing Cerius2 Saving models is discussed under Saving model structure files File formats are presented in File Formats The basics of starting Cerius and using its interface are demon strated in Introducing Cerius2 and described in The Cerius2 Interface Select the File Load Model menu item from the main control panel s menu bar to access the Load Model control panel 196 Cerius Modeling Environment April 1999 Directory selector popup Retum to run directory File selector list box Loading model structure files Cerius2 Models Cerius2 Resources Filename text
279. ion the default is CONTINUOUS CONTOURS contours A positive integer COLOUR GREY SCALE COLOR DIFFERENCE Color map The default is GREY SCALE CONVERSION LINEAR LOG Mapping function The default is LINEAR INTERP NEAREST LINEAR Interpolation system The default is NEAREST POLARITY POSITIVE NEGATIVE The default is POSITIVE LOWEST data value A real number This is the lowest color mapping value Cerius Modeling Environment April1999 431 D File Formats X Y graph ODB Initiation record Descriptors 2D graph ODB Initiation record HIGHEST data value Areal number This is the highest color mapping value EXPOSURE exposure A real number The default is 1 0 BRIGHTNESS brightness Arealnumber The default is 1 0 CONTRAST contrast Areal number The default is 1 0 gt GRAPH XY METHOD name version name and version Unique to this Graph These are very similar to data set name and version number SCALE FIXED AUTO XY NICE XY AUTO Y NICE Y The default is FIXED the specified range is used XMIN ordinate Notneeded for AUTO XY or NICE XY XMAX ordinate Not needed for AUTO XY or NICE XY YMIN ordinate Notneeded for AUTO XY NICE XY AUTO Y or NICE Y YMAX ordinate Not needed for AUTO XY NICE XY AUTO Y or NICE Y XLABEL string Text for the X axis label
280. ion and display Additional information To do this use the Property Maps control panel which is accessed by selecting the Property Maps button on the Isosurfaces control panel Specify a property to be mapped by choosing the desired grd or mbk file from the list box and clicking the LOAD pushbutton You can use the browser popup to access directories other than the cur rent one If more than one surface is displayed or has been loaded you may need to select the one on which to map the property using the list box on the Isosurfaces control panel Click the Add Property action button on the Property Maps con trol panel to display the property map You can vary the transparency of the displayed property map with the Transparency entry box You can change the range and color spectrum with which to dis play the property map by clicking the Preferences pushbutton to access the Property Maps Preferences control panel Please see the on screen help for details on the functioning of each control Editing and displaying slices Finding your surfacing files Slice specification and display To edit and display a 2D slice through the 3D grid of orbitals den sity or potential for your model use the Slices control panel which is accessed by clicking the Slices menu item on the ISOSUR FACES card If necessary choose the grid file to be analyzed by clicking the Files pushbutton to access the Isosurfacing File
281. ion button in the Table Groups control panel Please see the on screen help for details on the functioning of each control in the Table Groups control panel 356 Cerius Modeling Environment April 1999 Searching for information in a table Searching for information in a table Why read this section You should already know Accessing the tools Where to search What to look for You can use a search facility to locate cells containing information of interest You can specify relational operators and perform com parison operations and can save the result of the query as a table group or view the results as a subset view You can also replace found values with new values that you specify How to access the Tables module is described under Accessing the tools How to select a table for display and editing Specifying the current table and how to make sure control panels are connected to the desired table window Keeping track of the current table are dis cussed above Selecting columns and rows is discussed under Selecting rows and columns To search selected rows and or columns or the entire table you need to access the Find Cells control panel Click the FIND tool in the current table tool bar or Select the Data Find menu item from the TABLES card You can search all or part of the current table To search the whole table set the Find Within option to Entire Table To search within selected row
282. ion includes information on Using numbers Cross references Calculations on models Manipulating text Table and command operations Operators Available components that may be included in expressions are Unary math operators Binary math operators Statistical operators Statistical transformations Trigonometric operators Cross references Constants 5 gt gt gt gt gt gt o Unary model operators Cerus Modeling Environment April 1999 337 11 Working with Tables Using numbers Unary math operators Binary model operators Unary text operators Binary text operators Table operators gt gt gt Command operators Unary math operators Table 12 take one argument that must evaluate to a number Examples of expressions including unary mathematical operators are abs col 5 sqrt abs col 5 col 6 rand 20 The column references see To columns in this example all eval uate to numbers Table 12 Unary math operators in Cerius table expressions Operator Retums Description number Negation abs number Absolute value ceil number Retum the largest integer not less than x cbrt number Cube root exp number Exponentiation inverse of log fact number Factorial x floor number Retum the largest integernot greaterthan x frac number Retum the fractional part of x In number Natural log log number Natural log log10 number Log base 10 338 Cerius Modeling
283. ional contiguous rows or columns To select several noncontiguous rows or columns click the first row or column heading then lt Ctrl gt click each additional row or column heading that you want to select Your final selection may contain both rows and columns To select all cells in the current table do one of the following Click the SELECT ALL tool in the current table tool bar Click the top left cell in the table Select the Edit Select All menu item from the TABLES card To copy the contents of selected row s or column s or the current cell to the system clipboard for later pasting to a row column or cell respectively 322 Cerius Modeling Environment April 1999 Moving cutting one or more cells Pasting a column or row Technical notes on copy ing cutting and pasting Managing and editing tables Click the COPY tool in the current table tool bar See Pasting a column or row for pasting the copied information into a new location To clear cut the contents from selected row s or column s or the current cell and place them in the system clipboard for later past ing to a row column or cell respectively Click the CUT tool in the current table tool bar See Pasting a column or row for pasting the copied information into a new location To paste the contents of the paste buffer clipboard into selected row s or column s or the current cell Click the PASTE tool in the current
284. ironment menu item to access the Customize Environment control panel Check the Echo object reference check box Please see the on screen help for the precise syntax for entering subcriteria and for details on the functioning of each control in the Customized Atom Selection control panel The help that is accessed with the buttons on this control panel is context sensi tive that is what help is displayed depends on what the associ ated popups are set to The cumulative criteria are displayed in the Object Reference entry box as they are built up with the other con trols in this control panel The context of the Object Reference entry box may be edited Basic editing Why read this section Most models require some editing after the basic skeleton is built or while the model is being built You may also want to edit mod els that were read in from a file This section tells you where to 164 Cerius Modeling Environment April 1999 Related information You should already know Note Basic editing access the basic editing tools and how to perform tasks that are typically associated with editing a model It contains information on Changing atoms and their bonding types Editing the structure Refining the conformation Basic building tasks are presented under Basic building Tasks that may be less often or less typically performed such as editing atom attributes and changing defaults and preferences are cove
285. is Rotate current model about z axis Change stereo separation Stereo viewing Rotate selected atomsasgroup about y axis Translating and rotating atoms Rotate selected atomsasa group about x axis Rotate selected atomsasa group about z axis Change magnification of model view Changing the view magnification Mhe check mark indicates which mouse button to press 410 Cerius Modeling Environment April 1999 Keyboard shortcuts Table window Cursor over individual cell Table 32 Mouse actions when cursor is overa cell Key Operation Action click Make that cell and also itsrow and column current double click Same asclick and send command if any to Cerius Recalculating table values Mhe check mark indicates which mouse button to press Cursor over row orcolumn heading Table 33 Mouse actions when cursor is overa row or column heading Button Key Operation Action J click Select the entire row orcolumn JV drag line Change row height or column width Changing row column and heading sizes J double click Same asclick and send commands if any to Cerius Recalculat ing table values J lt Shift gt click Select from the last selection through the item clicked upon J lt td gt click Select an additional row orcolumn Mhe check mark indicates which mouse button to press Keyboard shortc uts This section summarizes what keys to press on your keyboard in order
286. is T Woo M OpenGL Programming Guide The Offi cial Guide to Learning OpenGL Release 1 Addison Wesley Reading Mass Chapter 6 1993 SHELXTL Reference Manual Siemens 157 1990 Todino G Strang J Learning the UNIX Operating System O Reilly amp Associates Inc Sebastopol Calif 1990 Cerius Modeling Environment April 1999 399 A References 400 Cerius Modeling Environment April 1999 Definitions Models fragments and templates Why read this section It is easy to get the terms fragment model template and molecule confused We have tried to be consistent in this documentation Definitions A fragment is a set of covalently bonded atoms A model is the entire contents of a Cerius model space The vis ible part s of a model may include A single atom One fragment for example a model of caffeine Several fragments that interact by noncovalent bonds or that do not interact for example a large solute fragment and many small solvent fragments A protein consisting of many residues and one or more sub units A receptor ligand complex A 1D periodic structure such as polyethylene or DNA A 2D periodic structure such as a regular surface A 3D periodic structure such as a crystal A template is a model or fragment that is used in building mod els Strictly speaking molecules exist only in the real world not in the simulated world of computational chemical mode
287. is of the contents of up to three columns How to access the Tables module is described under Accessing the tools How to select a table for display and editing Specifying the current table and how to make sure control panels are connected to the desired table window Keeping track of the current table are dis cussed above Selecting columns and rows is discussed under Selecting rows and columns To sort all or part of a table you need to access the Sort Table con trol panel Cerius Modeling Environment April1999 361 11 Working with Tables Specifying sort criteria Tip Specifying sort order How many rows to sort Click the SORT tool in the current table tool bar or Select the Data Sort menu item from the TABLES card To specify the primary sort criterion that is the column whose contents are used first for ordering the table enter the column name or number in the Sort First By entry box by Selecting the column or a cell in it in the table window or Choosing its name from the Sort First By popup in the Sort Table control panel For situations in which more than one row contains identical val ues in the column containing the primary sort criterion you can use one or two additional sort criteria Enter these columns names or numbers in the Then By entry boxes as described above for the first criterion You can set the first and second and third sort criteria by simply selectin
288. is perpendicular to the screen Translate the model by dragging over the model window with the middle mouse button depressed Scale the model by dragging over the model window with the middle mouse button and the lt Shift gt key depressed or with both the middle and right mouse buttons depressed Try rotating the model in some other display styles Then return the display style to Stick Note that rotation is quickest in the stick display Aside The Ellipsoid style is for models for which temperature factors have been defined The Polyhedra style is used to display coordinated cations for example in zeolites 2 Label the atoms in the model with their element type Change the Atom Labeling popup on the tool bar from No Label to Elements All the atoms in the model window should now be labeled as hydrogens or carbons either C or H If the display style isn t stick the labels may be difficult or impossible to see 54 Cerius Modeling Environment April 1999 Basic GUI Functions 1 135berz Troubleshooting If some of the atoms are not labeled you may have inadvertently selected some of the atoms in the model window If any atoms are selected then only those selected will be labeled To correct this click the Deselect All icon in the tool bar and then reselect Elements from the Display Style popup C Selecting atoms In the following steps you learn several techniques for
289. isplay style 45 249 ball 252 ball and stick 252 bond order 250 bonds 249 250 cations 253 cylinder 251 ellipsoid 254 inorganic systems 253 lone atoms 252 polyhedra 253 popup 28 space filling 252 stick 249 thermal ellipsoids 254 Distance tool 27 219 distances measuring 219 351 double click definition 131 double precision numbers 140 Draw with Hydrogens check box 158 drawing speed 258 dummy atoms 180 Edit Atoms control panel 162 Edit Bond tool 17 168 Edit Color Mappings control panel 275 276 278 Cerius Modeling Environment April 1999 439 Edit Color Ranges control panel 271 272 273 274 Edit Connectivity and Bonding control panel 168 171 181 250 425 Edit Elemen tool 166 Edit Element tool 16 Edit Elements control panel 180 265 Edit Formal Charge tool 167 Edit Hybrid tool 169 Edit Hydrogen Bonding control panel 171 183 184 Edit Selected Atoms control panel 167 181 189 Edit Temperature Factors control panel 189 editing models angles 172 atom positions 175 176 bond lengths 171 bond types 168 chiral centers 174 cleaning 178 cleaning preferences 190 comprehensive description 164 controlling the cleaning function 190 deleting atoms and bonds 170 elements 166 formal charge 167 hybridization 169 hydrogen bonds 183 minimizing 178 optimizing conformation 178 reasonable structure 178 refining conformation 178 rotating parts 176 symmetry 178 torsions 173 electron scattering 187 eleme
290. it Atoms menu item This gives access to the Edit Selected Atoms control panel Please see the on screen help for details on the functioning of each control in the Edit Selected Atoms control panel Changing the formal charge Specifying the formal charge Changing the formal charge Tip Changing the formal charge together with other properties Additional information Changing the bond type To change the formal charge on an atom use the Edit Formal Charge button in the Sketcher control panel Choose AUTO or the desired value of the formal charge from the popup to the right of the Edit Formal Charge tool Changing the default formal charge automatically activates the Edit Formal Charge tool If the formal charge is already correct you can activate the Edit Formal Charge tool by clicking it You can change the formal charge on atoms in the model window to the value specified by the formal charge popup in several ways Select the Edit Formal Charge tool and then pick the desired atom s Select the desired atom s Selecting atoms and groups of atoms and then double click the Edit Formal Charge tool To see the effect of changing the formal charge either click the H ADJUST button after changing the formal charge or check the Draw with Hydrogens check box before changing the formal charge You can also label atoms Labels according to their formal charge If you want to edit both the formal charge and oth
291. item to access the Display Attributes control panel Set the Style popup to BALL amp STICK The ball radii are proportional to the van der Waals radius of the respective atoms To set the ratio of ball radius to van der Waals radius click the Preferences pushbutton in the Display Attributes control panel to access the Style Preferences control panel Enter the desired proportion in the Ball amp Stick Ball Size entry box To set the radius of the sticks click the Preferences button in the Display Attributes control panel to access the Style Preferences control panel Enter the desired radius in the Stick Radius entry box Polyhedra are used to simplify structural display for inorganic systems that contain tetrahedrally octahedrally or square planar coordinated units for example zeolites the high Tc superconduc tors and multi molybdates Solid coordination polyhedra are drawn around cations the num ber of corners indicating the coordination number as defined by bonding connectivity To display cations as polyhedra you can Set the display style popup on the toolbar to POLYHEDRA or Select the View Display Attributes menu item to access the Display Attributes control panel Set the Style popup to POLY HEDRA Cerius Modeling Environment April 1999 253 8 Viewing and Displaying Models Displaying other atoms Thermal ellipsoids Understanding the display Specifying ellipsoid style Displayin
292. itions are not saved in this file For operating the file selector control in the Load Connolly Surface and Save Connolly Surface control panels please see Finding model file s Cerius Modeling Environment April 1999 225 7 Geometry Analysis Additional information Please see the on screen help for details on the functioning of each control in the Connolly Surfaces Load Connolly Surface and Save Connolly Surface control panels Vector properties Calculating vector prop erties Accessing the tools Displaying vector proper ties Additional information Vector attributes such as the force on an atom its velocity or its electron spin state can be displayed as arrows at all or selected atoms Vector attributes are output by other Cerius modules such as the quantum chemistry modules which are licensed and documented separately Access the Vector Properties control panel by selecting the Geom etry Vector Properties menu item in the main control panel s menu bar You use this control panel to display vector properties on all or selected atoms in your model You can use the Vector Properties control panel to show remove or hide available vector properties If you want to edit the style or size of the displayed vectors click the Preferences pushbutton to access the Vector Preferences control panel Please see the on screen help for details on the functioning of each control in the Vector Proper
293. itmap resolution for printing graphs Changing the bond type Refining the conformation Editing a property color map Creating and editing anew color range Recording commands Selecting data to plot Assigning data types Apparent depth effects Applying mathematical expressions to cells or col umns Concepts Ball and stick models Dummy atoms Type a C in the sketch 402 Cerius Modeling Environment April 1999 Glossary additional word meaning information formalcharge The difference between the number of electrons possessed by the neutral isolated atom and that formally possessed by the atom within the mole cule assuming that electrons in covalent bonds are shared equally between participating atoms and that no sharing of core and lone pair elec trons occurs fractionalbond A quantitative measure of the orderofa bond E order which may for example be related to overa p integralsin the molec ula r orbital description of the system gallery The graph window Displaying and editing graphs graphics quality Related to the color interpolation between facets Graphics quality used to draw curved surfaces graphicsresolu Related to the number of facets used to draw Object resolution tion curved surfaces group A named set of atoms Defining and selecting groups group A named set of table cells Grouping table information initia lization A command script that is run automatically when Starting Cerius2
294. ius Modeling Environment April 1999 Example Loading a template Basic building Using the file browser to navigate the directory structure is fairly intuitive The procedure is described under Loading model structure files A specific example of using the file browser to find and load a tem plate is demonstrated under The Templates button looks like Once you find the desired template file load it by Selecting its name and then clicking the LOAD button or Double clicking its name The new name should appear next to the template tool and the template tool becomes active as indicted by highlighting Adding templates to a model Custom templates Once the desired template is chosen see Selecting templates click the template tool to activate it if it is not already active The cursor is now shaped like a T when it is over the model window You can use the template to start building a model or to add a group to an existing model To add the template as a separate or new fragment click in empty space To add the template at an existing atom pick that atom It is attached in a reasonable way e g by replacing a hydrogen To add identical templates simultaneously to several atoms first select the atoms Selecting atoms and groups of atoms and then double click the template tool or single click if it is already active Hydrogen atoms are replaced as appropriate If you often need a particu
295. jour nal Acta Cryst C by the International Union of Crystallography Ata minimum the file must contain either unit cell parameters or atom coordinates Cartesian and atom types or atom labels To utilize space group information the file must include symmetry positions and either International Tables IT number OR cell setting If space group information is not used the file must include both cell setting and space group name so that the lattice type and the lattice centering can be found Cerius reads cell setting space group name symmetry positions unit cell parameters atom labels atom types if present if not get from atom labels and _atom_ type_symbol if present atom coordinates fractional occupancies isotropic temperature factors isotropic anisotropic flag anisotropic temperature factors connectivity 422 Cerius Modeling Environment April 1999 Struc ture files CSSR Record 4 50n one per atom Fomat 38X 3F8 3 21X 3F8 3 4X SPGR 13 1X A11 214 1X A60 A53 14 1X A4 2X 3 F9 5 1X 814 1X F7 3 SERC Daresbury Laboratory s Cambridge Structure Search and Retrieval CSSR files contain information very similar to CAM BRIDGE files but were developed to be easier to create read and edit manually Suitable for storing nonperiodic 2D and 3D structures CSSR files can store Cartesian or fractional coordinates of atoms and their ele ment
296. k any point on the dials and or enter angles in degrees in the entry boxes Dragging a slider is the least exact of these methods and entering an angle the most You can orient the view so that selected atoms in the current model lie parallel or perpendicular to the computer screen To do this select the View Orient menu item to access the Ori ent View control panel Select the desired atoms Click the Parallel To Screen or Perpendicular To Screen action button All visible models rotate in concert around the same axis and by the same angle The model view is reoriented so the best fit plane through the selected atoms is lies in or perpendicular to the plane of the com puter screen Please see the on screen help for details on the functioning of each control in the Viewing Dials Orient View and View Options con trol panels Mouse functions and keyboard shortcuts are summa rized in Mouse and Keyboard Actions Changing the view magnification Manual zooming To interactively change the view scaling of models you can place the cursor in the model window and Hold down the middle and right mouse buttons and drag the cursor in the model window or Hold down lt Shift gt plus the middle mouse button and drag the cursor in the model window 234 Cerius Modeling Environment April 1999 Filling the model window Maximum size Normal model window size Incremental zooming Lale gt Moving models o
297. l color if desired by entering its position in the entry box for Add a new critical color and then defining the color by using the sliders If you subsequently decide to increase the number of entries in the range critical colors in the interior of the range maintain their approximate relative positions for exam 272 Cerius Modeling Environment April 1999 Saving a color range Additional information Editing a color range Caution Accessing the tools Selecting the color range Editing the color range Customizing display colors ple a critical entry at position 7 in a 16 color range becomes posi tion 14 if you increase the number of entries to 32 To change the position of a critical color other than one of the end colors enter a new position number in the entry box for Move selected critical color You can save a custom color range by saving the current Cerius session see Saving the current session Please see the on screen help for details on the functioning of each control in the Edit Color Ranges control panel You should edit only color ranges that you create You should never delete or rename the color ranges that are supplied with Cerius because many automatic Cerius functions require the supplied ranges to be present and have the correct name However you may change the colors that are used in the supplied color ranges Select the Utilities Customize Color Ranges menu item from the m
298. l panel Cerius saves tables in MSI tbl format and automatically adds tbl to the filename if you have not specified some other extension Closing a table Closing a table You may remove any unwanted tables from the current Cerius session at any time by closing them To close the current table you can Click the CLOSE tool in the table manager tool bar or Select the File Close menu item from the TABLES card Table style and display When you create a new table or when a Cerius application gener ates a table the cells have a default set of properties Many table properties can be modified to meet your specific requirements for how your data is displayed You can modify the properties of all cells in a table of the cells in the current selection or of the cells in a named group Cerius Modeling Environment April 1999 327 11 Working with Tables Finding information This section includes information on Aligning information within columns Assigning data types Setting display formats Specifying headings and banners Changing row column and heading sizes You should already How to access the Tables module is described under Accessing the know tools How to select a table for display and editing is discussed under Specifying the current table How to select columns Selecting rows and columns and make a cell current Selecting a cell are described above Aligning information within colum
299. l s click the DIS PLAY pushbutton in the Panel Manager control panel To close all open control panels click the HIDE pushbutton that is located in the All Visible Control Panels area of the Panel Man ager control panel near the top 392 Cerius Modeling Environment April 1999 Deactivating control pan els Cascading contro panels Automatic panel display Cancelling automatic panel display Saving control panel con figuration How it works Interface configuration To close only selected open control panels click the HIDE push button that is located in the Selected Panels area of the Panel Man ager control panel Alternatively to close all open control panels click the clear panels tool l on the toolbar of the Visualizer main panel To remove a selected control panel s name from the Active Control Panels list click the REMOVE pushbutton This action does not hide the panel if it is open To add a control panel s name to the Active Control Panels list close it if it is open by clicking that panel s close box qj and then open it by using the usual menu bar or card menu item To group all open control panels into an orderly cascade click the CASCADE pushbutton in the Panel Manager control panel Alternatively to cascade all open control panels click the cascade panels tool i on the toolbar of the Visualizer main panel If you commonly use the same control panels during a Cerius
300. lar template that doesn t exist you can construct it as a model and save it as a custom template How to do this is discussed more fully in the presentation of the Analog Builder in Cerius Builders since that builder can both check a tem plate structure for some errors and save it Cerius Modeling Environment April 1999 155 5 Building Models To save a template if you don t have the Analog Builder follow these steps 1 Construct the template model making sure you are satisfied with its final structure and conformation this section 2 Decide which hydrogen atom should be the point at which the template is to be added to other models 3 Replace this hydrogen with a dummy element of type X Changing the element type 4 Save the model in msi format Saving model structure files You should now be able to use your template just as you do any other template except that the Sketcher Template control panel does not find it automatically unless you were able to save it in the default Cerius2 Models templates directory Fusing and connecting fragments Fusing fragments The Sketcher control panel includes tools for fusing or connecting two entities to form one model Fusing two fragments in the model window means to join them so as to delete a heavy non hydrogen atom For example two benzenes could be fused to form naphthalene or many cyclohex anes and cyclopentanes could be fused in building buckminster
301. lay mode all the single atom picking and selection rect angle methods listed above Single atom picking can be used to select atoms in all displayed models In border mode all the single atom picking methods listed above Single atom picking can be used to select atoms in all dis played models The selection rectangle methods function only for the current model see Specifying the current model Ingrid mode all the single atom picking methods listed above Single atom picking can be used to select atoms in all displayed models Selecting and deselecting collections of atoms Selecting according to properties Pick target What is selected A single pick in the model window by the same selection process as described under Selecting and deselecting individual atoms can act on different pick targets A single click can pick a single atom all atoms in one residue all atoms in one chain or all atoms in one model Similarly using a selection rectangle can pick only the atoms within the rectangle or all residues chains or models that have at least one atom within the rectangle To change the default behavior i e picking individual atoms change the pick target popup on the toolbar see The controls from Atom to Residue Chain or Model Residues and chains are not present in all models but may be defined in other Cerius mod ules which are documented separately When you pick a target other items in addition
302. le see Sketching an iron atom I Adding the correct number of hydrogens see Correcting the hydrogens see also Adding hydrogens Cerius Modeling Environment April1999 47 2 Introducing Cerius LI Cleaning up the conformation see Cleaning up the conformation see also Refining the conformation LI Using file browsers to find models and templates see Stop when you see the filename methyl Reading in more models see also Man aging Models and Sessions Q Saving and loading models see Saving your caffeine model Read ing in more models see also Managing Models and Sessions T Labeling a model see Labeling a model see also Labeling and annotating models QO Moving a model see Moving a model Zooming in or out on a model Returning the model to the center of the model window see also Moving models on the screen QO Changing a model s display style see Changing the display style see also Model display style QO Selecting atoms and groups of atoms see Selecting atoms see also Selecting atoms and groups of atoms I Measuring parts of a model see Measuring components of the model s geometry see also Geometry Analysis I Managing multiple models see Adding a new model space Read ing in more models Managing multiple models see also Handling multiple models m Coloring a model according to atomic properties and creating property maps see Coloring atoms according to a property see al
303. leaned Refining the conformation etc This enables you for example to position a fragment inside a larger structure while monitoring close contacts between the two or to monitor close contacts during minimization Please see the on screen help for details on the functioning of each control in the Close Contacts control panel Model surfaces Connolly surfaces What is a Connolly sur face You can use the Connolly 1983a b surface utility to probe a mol ecule surface or crystal to produce a dot display of the contact surface You can use this utility for example to map out the inter nal channel structure of a crystal find the solvent accessible sur face of a large model or understand the topography of a 2D surface You can use the Connolly surface utility to calculate and display a van der Waals or a Connolly surface for all or part of a model A Connolly surface is the van der Waals surface of the model that is accessible to a solvent molecule having a nonzero radius The surface is generated by rolling a spherical probe of a specified radius over the van der Waals surface of the model Figure 2 Cerius Modeling Environment April 1999 223 7 Geometry Analysis A van der Waals surface is generated when the probe radius is Zero Figure 2 Generation of Connolly surfaces Dotted lines represent the van der Waals surfaces of the model and the probe the solid blackline representsthe Connolly surfac
304. lease see the on screen help for details on the functioning of each control in the Graph Manager control panel Selecting data to plot Related information Accessing the tools Selecting the data Any Cerius data set s currently in the computer memory can be selected and plotted in a new graph However the data set must be compatible with the type see Specifying the type of graph of graph specified In addition only Cerius data sets can be plotted in newly created Cerius graphs Loading graphs containing data sets is discussed in Loading graphs Generating data for graphs is discussed in the documentation for the relevant application modules If you already have the Gallery Manager control panel open Accessing the tools click the Graph Manager pushbutton in the Gallery Manager control panel to access the Graph Manager con trol panel Alternatively select the Graph Manager menu item from the GRAPHS card to access the Graph Manager control panel To add a data set to the new graph check the Display check box es next to the names of the data sets that you want to display in the currently editable graph The name of this graph appears Cerius Modeling Environment April 1999 295 10 Working with Graphs Additional information Tip near the top of the Graph Manager control panel You can only select data sets that are of the appropriate type Specifying the type of graph Please see the on screen hel
305. led use the Row or Column pane respectively of the Table Properties control panel Check the Lock Row Scroll or Lock Column Scroll check box respectively and click the APPLY TO pushbutton Please see the on screen help for details on the functioning of each control in the Table Properties control panel Changing row column and heading sizes Changing column width and row height You can change the width of any column including the column containing the row headings and can change the height of any row including the row containing the column headings To resize a column drag the line to the right of a column in the col umn heading area of the current table display The cursor changes to red double arrows to indicate it is over the line Alternatively access the Table Properties control panel as above see Accessing the tools and set the Properties popup to Column Enter the desired width in the Column Width entry box and click the APPLY TO pushbutton 332 Cerius Modeling Environment April 1999 Changing heading sizes Using grid lines Additional information Values and mathematical expressions To resize a row drag the line below a row in the row heading area of the current table display The cursor changes to red double arrows to indicate it is over the line Alternatively access the Table Properties control panel as above see Accessing the tools and set the Properties popup to Row Enter the desired he
306. lements deute rium and other nonstandard elements are listed at the bottom of the Periodic Table window You can access the periodic table by clicking the periodic table icon in several control panels including the Edit Elements control panel To find the atomic number atomic mass symbol and name of any real or dummy element click the element in the Periodic Table window This information is listed in a box near the top of the window below the line stating what control panel the periodic table is linked to 180 Cerius Modeling Environment April 1999 Atom properties Additional information Bond properties Editing bonds Accessing the tools Additional information Advanced building and editing You can also edit properties of individual selected atoms rather than of all existing and future atoms of a given element type the element type hybridization state Changing the hybridization and adjusting the valence charge formal charge mass occupancy the atom name and temperature factors Specifying temperature fac tors To do so select the Build Edit Atoms menu item to access to the Edit Selected Atoms control panel Please see the on screen help for details on the functioning of each control in the Edit Selected Atoms control panel Most of these atom properties can alternatively be specified before placing an atom in the model window with the Add Atom control panel Precise positioning of atom
307. lent to setting the Latitude and Longitude both to 0 0 Illuminate from the lower right front by setting the X and Z directions to positive values and the Y direction to a negative number The absolute values of these numbers are unimportant since you are a defining only a direction not a position however their ratios do affect the direction Move the light source upwards by increasing the value of the Latitude Swing it around to the left by decreasing the Longitude Illuminate from directly behind your model by setting the X and Y directions to 0 and the Z direction to a negative number This is equivalent to setting the Latitude to 0 0 and the Longi tude to 180 284 Cerius Modeling Environment April 1999 Positional lights Accessing the tools Changing the location of the light How it works Tip Lighting control Positional lights can often be used to increase the perceived three dimensionality of a scene Concepts In addition they can be con verted to spotlights Spotlights To set up a positional light located within the scene click the Position pushbutton in the Lighting control panel to access the Lightsource Position control panel Select the Light is Positional control You can change the light s location by using any combination of the X Y Z Latitude Longitude and Radius controls You can for example Illuminate from a light positioned directly to the right of
308. lication modules Unlike many dedicated spreadsheet programs the Cerius table facility understands and can make calculations that refer to molecular 312 Cerius Modeling Environment April 1999 You should already know Accessing the tools Additional information models However the Cerius table facility does not have all the features of a typical dedicated spreadsheet program Therefore you can export Cerius tables for further study to programs such as Microsoft Excel You can also import tabular data from ASCII files into a Cerius table for further manipulation and display The basics of starting Cerius and using its interface are demon strated in Introducing Cerius2 and described in The Cerius2 Interface Tables in Cerius are produced as output from calculations in var ious other application modules How to set up and run the appro priate calculations are discussed in the documentation for the relevant application modules The tools for handling tables are accessed from one of the decks of cards in the main Visualizer control panel To access the Tables module click the deck selector see also Access to application mod ules and choose TABLES amp GRAPHS from the list that appears If the TABLES card is not already in front of the GRAPHS card click the title of the TABLES card The deck of cards menu area should look like Please see the on screen help for details on the functioning of each c
309. lick the Connect tool Bonds can be formed only one at a time You can also connect fragments with the Sketch with tool see What next Adding hydrogens Note This section refers to using the Sketcher control panel The 3D Sketcher unless otherwise indicated You may add hydrogens to your model at any time and in several ways Wait until you have finished building and editing your struc ture then click the H ADJUST button Hydrogens are added to or deleted from all atoms as needed in the current model so that their valences are satisfied Cerius Modeling Environment April 1999 157 5 Building Models Hybridization state Select the Hydrogen tool and then pick atoms whose valences you want to satisfy by adding or deleting hydrogens Alterna tively select these atoms first Selecting atoms and groups of atoms then double click the Hydrogen tool Check the Draw with Hydrogens check box Hydrogens are automatically added to or deleted from atoms as you sketch your model Use the Sketch with tool with the Sketch with entry box set to H Adding atoms and bonds Use the Add Atom control panel Precise positioning of atoms during building if you need to control hydrogen positions exactly Change selected atoms to H using editing tools Changing the element type To delete all hydrogens select hydrogens by element Selecting and deselecting individual atoms then use the Delete Atom
310. ling Cerius Modeling Environment April 1999 401 B Definitions Glossary Some other words that have specific meanings within Cerius are listed below additional word meaning information ambient light Light impinging ona scene from all directions Concepts balloon help Small explanatory text boxes displayed when the Balloon help bitmap resolu tion bond type charge cleaning a model colormap colorrange command script A file of Ceru commands that can be used to data set data type depth cueing derivation diffuse lighe display style dummy atoms enter cursor lingers overa control Number of dots per inch used in printing graphs Associated with the nature and number of shared electrons between atoms e g single double partial bond types The overall partial charge on an atom Optimizing the model conformation Defined corelation of properties with a color range Defined sets of colors control future Cerius sessions A set of related points in a graph forexample all the points belong to one curve Real numbers Booleans text etc ina table Representation of aerial perspective Mathematical expression in table cells Light scattered from an object in all directions Display of atoms and or bonds as sticks balls etc Nonstandard elements with defined properties Type some characters then press lt Enter gt orclick anywhere else in the control panel B
311. lipsoid axis click the Prefer ences pushbutton in the Display Attributes control panel to access the Style Preferences control panel Check or uncheck the Show Principal Axes check box Similarly to show or hide bonds check or uncheck the Show Bonding check box You can define a scaling factor for the display size of thermal ellip soids A value of 1 0 corresponds to an ellipsoid whose radius at any point on the surface is equal to the root mean square rms atomic vibration in that direction At a scaling factor of 1 0 the 254 Cerius Modeling Environment April 1999 Model display style probability of the atom actually lying within the ellipsoid is low Greater values produce greater probabilities as shown in Table 7 Table 7 Relation of thermal ellipsoid size to atom location Scale factor Probability of atom being within ellipsoid 1 54 50 2 02 75 2 50 default 90 2 80 95 3 37 99 Setting the size To set the scale factor for thermal ellipsoids select the View Dis play Attributes menu item to access the Display Attributes con trol panel Click the Preferences pushbutton in the Display Attributes control panel to access the Style Preferences control panel Enter the desired scale factor in the Ellipsoid Size entry box Structure traces You can make only a structural trace of a model visible This is done differently depending on whether the model is a protein or any other kind of polymer Vi
312. lled the model window Click once near the center of the model window A benzene fragment appears but it is not oriented conveniently Move the cursor so it s near any edge of the model window Then hold down the right mouse button and move the cursor parallel to the closest edge of the window until one of the dou ble bonds is vertical and on the right side of the fragment The model should now look something like this 10 Cerius Modeling Environment April 1999 Note Building a model caffeine Atoms are color coded in the model window the grey bonds connect two carbon atoms and the half grey half white bonds connect hydrogens white with carbons grey Atoms are not emphasized in the current display style but one is located at the end of each bond Click the Sketch with tool The Sketch with tool looks like The control panel indicates that you will sketch with C whereas the ring you want to add contains 2 N s and only one C So it might be more efficient to sketch with N instead of C Locate the popup control to the right of the Sketch with C entry box In other words this control Cerius Modeling Environment April1999 11 2 Introducing C erius Am Sketch with eae E Click the popup control then while continuing to hold the left mouse button down drag the cursor down and then release it over the N In other words Cho
313. lly You can also examine torsions or the angle between any two planes with the Measurements control panel Torsions To change a torsion angle precisely select the Move Bond Geom etry menu item to access the Bond Geometry control panel Please see the on screen help for details on using the controls in the Bond Geometry control panel to measure and change torsions bond lengths and valence angles and to specify which atoms are moved in the process You can also change torsions by rotating parts of models to speci fied orientations Rotating atoms precisely You can examine tor sions or the angle between any two planes with the Measurements control panel Torsions For inverting a chiral center please see the next section You can implicitly control default torsion angles through setting the hybridization state of the atoms involved Changing the hybrid ization and adjusting the valence Inverting about an atomic center The most straightforward way of inverting about a chiral center is to use the Invert tool in the Sketcher control panel Although inversion can be applied to any atomic center it should be most useful when the center is chiral You can Select the Invert tool and then pick the atomic center whose chirality you want to invert Two fragments attached to that 174 Cerius Modeling Environment April 1999 Note Basic editing atom are rotated 180 about the axis that bisects the bond angle be
314. lor with the background color for objects that appear to be farther behind the surface of the computer screen The extent of depth cueing can be changed Select the View Graphics Depth Cueing menu item to access the Depth Cueing control panel To adjust the degree of depth cueing use the Depth Cue Factor slider or its associated entry box A value of 1 means that appar ently near and far objects are all drawn with full color intensity a value of 0 means that far objects disappear into the background To change the apparent distances at which objects are drawn with full or minimal color adjust the Near Distance or Far Distance controls respectively Please see the on screen help for details on the functioning of each control in the Depth Cueing control panel The projection method is another way of enhancing the appear ance of depth in models Two methods are available Inan orthographic projection an object appears to be the same size at any apparent distance behind the surface of the com puter screen The observer is assumed to be infinitely distant that is the projection lines are parallel and normal to the screen Ina perspective projection the object size diminishes with dis tance so that for example parallel lines perpendicular to the computer screen would meet at some apparent distance behind the surface of the screen The angle for perspective viewing can be set to produce narrow or wide fish eye proje
315. lready know You can define any subset of columns and or rows as a group and give that group a name Named groups are stored in the table file when you save the table to disk This section includes information on Creating a named group Editing a group definition Selecting named groups Deleting a group definition Groups can be used in several ways in the Cerius table window You can Refer toa named group of numeric cells in statistical expres sions Statistical operators View only a named group by collapsing the display of the table Viewing subsets of a table Plot the data in a named group Graphing table information Restrict a search to a named group Searching for information in a table Sort the rows in a named group made up of rows Sorting table information Export a named group as a subset of the table to a new file Exporting table information How to access the Tables module is described under Accessing the tools How to select a table for display and editing Specifying the current table and how to make sure control panels are connected to the desired table window Keeping track of the current table are dis cussed above Selecting columns and rows is discussed under Selecting rows and columns Cerius Modeling Environment April 1999 353 11 Working with Tables Creating a named group Creating a named group from a selection Defining the entire table as a named group
316. lso change how bonds are calculated see Editing element and bond attributes select the Build Edit Bonds menu item This gives access to the Edit Connectiv ity and Bonding control panel Please see the on screen help for details on the functioning of each control in the Edit Connectivity and Bonding control panel Set ting the bond calculation preferences is discussed under Bond prop erties Changing the hybridization and adjusting the valence Generally Cerius automatically determines what the hybridiza tion should be However you can specify the hybridization man ually 168 Ceru Modeling Environment April 1999 Basic editing To change the hybridization for any selected atom use the Edit Hybrid tool Tip Specifying the hybridiza tion Changing the hybridiza tion Other ways to change the hybridization You can label atoms Labels according to their hybridization Choose the desired type of hybridization from the popup to the right of the Edit Hybrid tool AUTO means to allow Cerius to automatically determine the hybridization the specific types listed in the popup are self explanatory OTHER should be used for high coordination centers not specifically included in the list of choices Setting the hybridization to OTHER where appropriate allows the cleaning function Refining the conformation to work optimally Changing the default hybridization type automatically activates the Edit Hybrid
317. ly need to know nothing about this process you may want to learn about creating and using Cerius commands to facilitate performing a series of related or identical tasks in an automated way You may also want to know about Cerius s facilities for running application modules on remote machines and for managing licenses This section contains information on Command logging and scripting Controlling Cerius2 from scripts Managing licenses Running application modules externally Table 25 Finding information about scripts and lic ensing If you want to know about Read Initia lization startup scripts Starting Cerius2 with a command script file Performing repetitive or routine tasks Playing back scripts and log files Starting Cerius2 with a command script file Recording aallorpartofa Cerius ses Recording commanas sion Cerius Modeling Environment April 1999 375 13 Scripts and Licensing Table 25 Finding information about scripts and licensing If you want to know about Read Starting and saving C erus sessions Working with Cerius2 sessions Other ways of setting preferencesand Using saved sessions as preferences settings Customiz customizations ing the Interface Running Cerius without its graphics Starting Cerius2 with a command script file You should already The basics of starting Cerius and using its interface are demon know strated in Introducing Cerius2 and described in The Cerius2
318. m the point at which you saved the session you just loaded Loading individual models is described in Loading model structure files Using saved sessions as preferences settings Saving preferences in a session file Loading only preferences from a saved session If you often need to change many settings before starting your work you can load only the application preferences from a saved session file Nondefault application settings are saved when you save a session What is saved as a session However not all applications save all nondefault control settings when a session is saved You may want to start up one of your typical sessions by changing all settings as desired in the absence of any models Then you can save this empty session Although you can load only the preferences from any session file saving an empty session may depending on how you work decrease disk space requirements Before loading or building any models load your preferences by Loading Loading a previously saved session an empty session file or 214 Cerius Modeling Environment April 1999 Working with C erius sessions Checking the Preferences Only check box in the Load Session control panel and then loading any desired session file Wami PA Loading an empty session file or loading only the preferences from any session file removes all models and associated data from your current session Therefore you need to l
319. ment from the popup immediately to the right of this text entry box This popup lists several commonly used ele ments Select the periodic table tool to the far right of this text entry box When the Periodic Table window appears select the desired element If the Periodic Table window is already open click the periodic table tool to link it to the Edit Element function The Periodic Table window can function with any of several controls or control panels The control or panel that it is currently linked to is listed near the top of the Periodic Table window To change the link and therefore also the entry box that the periodic table affects click the appropriate periodic table tool in the desired control panel Changing the default element type automatically activates the Edit Element tool If the edit element type is already correct you can activate the Edit Element tool by clicking it You can change atoms in the model window to the element type specified in the element type entry box in several ways Select the Edit Element tool and then pick the desired atom s Select the desired atom s Selecting atoms and groups of atoms and then double click the Edit Element tool 166 Cerius Modeling Environment April 1999 Changing the element type together with other properties Additional information Basic editing If you want to edit both the element type and other properties simultaneously select the Build Ed
320. metric operators statistical operators and trans formations binary and unary molecule operators and command operators The expression can return that is generate numbers text or models This section includes information on Cerius Modeling Environment April 1999 333 11 Working with Tables You should already know Applying mathematical expressions to cells or columns Entering mathematical expressions Recalculating table values How to access the Tables module is described under Accessing the tools How to select a table for display and editing is discussed in Specifying the current table How to select columns Selecting rows and columns and make a cell current Selecting a cell are described above Applying mathematical expressions to cells or columns Concepts Technical notes The following terms define the relationship between values and mathematical expressions derivations in Cerius tables Value tThe information displayed in any cell A cell can con tain numerical text or model data Derived value The value displayed in a cell that results from the evaluation of an expression Derived cell A cell whose contents are derived from an expres sion applied only to that cell Derived column A column in which all cells display values derived from an expression applied to the entire column Label A text description you can apply to a row or column as a whole Columns a
321. ming pro cesses Exit option Exit and rename logfile Ignore request Information sources Interrupt Typical controls include Ignore or Ignore request Command processing continues from the point at which it was interrupted Stop Current Process ASAP The tool or application stops processing as soon as possible that is when Cerius determines that it can do so cleanly Exit Session Immediately The Cerius session is ended immediately When Cerius is busy processing a command issued from the Visualizer or an application module a Cerius message window indicating the status of the job may be displayed This window can take several forms depending on the nature of the command in process In some a moving bar indicates progress In others where progress is less easily quantifiable a diamond shaped activity indicator appears During such periods of prolonged activity you cannot perform any other Cerius tasks except basic mouse controlled model viewing actions If the command in process can be stopped cleanly before its scheduled conclusion the message window contains an INTERRUPT button Cerius Modeling Environment April 1999 143 4 The Cerius Interface When Cerius is iconified Other windows Click the INTERRUPT button if present to stop processing the command A warning window see Warnings with several options appears giving you the chance to confirm your choice or chan
322. mmand in a control panel Click the Preferences button on the Display Attributes control panel to open the Style Preferences control panel 58 Cerius Modeling Environment April 1999 Basic GUI Functions Again control panel buttons with names ending in ellipses open other control panels Right mouse Click with the right mouse button on a command in one of a button for help the control panels This brings up a help text panel that describes the function Click in the help text panel to close it Try clicking with the right mouse button in other items in the GUI check boxes buttons popups sliders menu items and so on 4 Access the Stereo control panel from a pullright menu Select View Graphics gt and then move the mouse to the right to select the Stereo item on the pullright menu The Stereo control panel opens You would use the Stereo view control panel if you wanted to view the model as a stereo pair or with the Crys taleyes stereo hardware Right arrows at the end of pulldown items indicate that there are pull right menus for these items 5 Move and resize control panels Click and drag some control panel title bars to different screen locations Cerius Modeling Environment April1999 59 3 Tutorials Resize some control panels by clicking and dragging their edges or corners Cascade Click the Cascade Panels button on the to
323. mmetry information is loaded as space groups unless the information is nonstandard in which case spe cial position information is provided For details refer to the ICSD User Manual 1991 Section 9 MACC Y Molfile 3 4 Record MDL s MACCS file format is widely recognized by modeling pro grams and chemical information systems MACCS files default file extension mol are similar to CSSR files but are not suitable for periodic models as they do not store unit cell parameters or frac tional coordinates Bond order information is stored but not used by Cerius MACCS files consist of four standard records plus one record for each atom and each bond These records are described in terms of FORTRAN edit descriptors in the table below Format Stores 20X A2 213 Title A line of text description for the file Dimensionality The dimensionality of coordinates this is always 3D for MACCS files output by C eru Unused Numberof atomsand bonds Total numberof atomsand total number of bonds in the file 5 onwards one for 3F10 5 1X A2 Atom coordinates and elements X Y Zc oordinates each each atom then foreach bond 313 atom element type Bonding The serialnumbersof the two bonded atomsand the orderof the bond between them 424 Cerius Modeling Environment April 1999 Struc ture files MolEN Support for the Enraf Nonius MolEN file format default file extension xyz is provide
324. mn s whose values you want to plot on the y axis and assure that the Selection control on the left is selected You can plot every column in the table by selecting the Entire Table control on the left side of the control panel If groups are present Grouping table information you can plot only columns contained in a group by selecting Group on the left and choosing the group name from the associated popup The procedure is analogous if you set the Y Axis popup to Rows To specify the data to be used as the x axis choose a column name or number from the X Axis popup To plot all values in the table select the Entire Table control on the right side of the control panel You can restrict the x axis to a part of the specified column by selecting the desired rows and selecting the Selection control on the right side of the control panel or by selecting Group on the right and choosing a group name Grouping table information from the associated popup You could for example plot all columns within a restricted range of values along the x axis by selecting Entire Table on the left and Selection on the right If the x axis is anything other than the row index numbers you probably want to sort Sorting table information the table using the column that you will use as the x axis as the primary sort criterion The procedure is analogous if you set the Y Axis popup to Rows In this case only rows appear in the X Axis popup T
325. modules for example Receptor CASTEP UI Gaussian UI and MOPAC UID enable you to generate surfaces and then adjust their transparency How to create surfaces is found in the documentation for the rele vant application modules To set the style with which surfaces are made transparent select the View Display Attributes menu item to access the Display Attributes control panel Cerius provides two methods for applying transparency to sur faces Set the Transparency Method popup to PATTERN or BLEND 278 Cerius Modeling Environment April 1999 Additional information Lighting control Blend transparency can be compared to looking at the model through a surface made of fine silk cloth Pattern transparency gives a screened effect where the overall transparency is an average of a net of opaque and transparent areas on the surface Please see the on screen help for details on the functioning of each control in the Display Attributes control panel Lighting contol Important Finding information Related information Cerius has enhanced lighting capability that also can aid in understanding your model s 3D structure and in spotlighting cer tain features You must be running Cerius in OpenGL mode in order to use all the lighting controls documented in this section On Silicon Graphics machines OpenGL mode is used by default or is available for Indy machines those with XL or Impact graphics and all with
326. mperature factors in files File Formats Cerius supports the import and export of a wide range of com mon file formats for the storage of atomic coordinates and associ ated data This facility enables you to interface with other molecular modeling and computational chemistry programs including procedures you have written yourself This section briefly describes the file formats supported in Cerius MSI Molecular Simulations native Cerius format CAR MDF ARC COR Molecular Simulations native Insight II formats Documentation can be found elsewhere in http www msi com doc MSF Molecular Simulations QUANTA structure file format BGF Molecular Simulations BIOGRAF file format CAMBRIDGE read only Cambridge Crystallographic Data base FDAT format CIF read only Crystallographic Information File CSSR SERC Daresbury Laboratory s Cambridge Structure Search and Retrieval file format 2 ICSD read only Inorganic Crystal Structure Database MACCS Molfile MDL s MACCS file format MolEN Enraf Nonius MolEN file format MOPAC MOPAC AMPAC file format PDB Brookhaven Protein Data Bank format SHELX SHELX structure file format Information on storing temperature factor information in structure files of various formats Loading and saving temperature factors in structure files Cerius Modeling Environment April 1999 415 D File Formats Graph files Grf Mole
327. mputational results obtained using software programs from Molecular Simu lations Inc dynamics calculations were done with the Discover program using the CFF91 forcefield ab initio calculations were done with the DMol pro gram and graphical displays were printed out from the Cerius molecular mod eling system To reference a Molecular Simulations publication in another publication no author should be specified and Molecular Simulations Inc should be considered the publisher For example Cerius Modeling Environment April 1999 San Diego Molecular Simulations Inc 1999 Contents 1 How Use This Guide 1 Who should use this guide 0 0 0 0 cece eee eee 2 Additional information sources 0 0 00 c eee ees 2 Other Cerius documentation susse reece eevee 3 Typographical conventions 0 0 00 cece eee 3 2 Introducing Cerius 5 Starting Certs Dac ecunera nena eae EE A BA 6 Building a model caffeine 1 0 cece ee 8 Saving a model zend eTe eee eee 21 What you can do with a model display 23 Building another model ferrocene 055 32 Reading in additional models 000005 35 Managing multiple models 0 0000 c eee eee 36 Printing amodel seims 0 0 6 c ccc eee 41 Controlling the 3D display s asasan sannan eee eee 42 Exploring Cerius on VOUT OWN eee eee eee 45 Summary Some of what you ve learned 47 3 Tutorials 49 Basic GUI Fu
328. n Table list box Assure that the Selection tool is selected and click the REMOVE pushbutton Please see the on screen help for details on the functioning of each control in the Table Groups control panel Selecting named groups Selecting groups Related information Additional information You can select a group either to use it in some task or as a way of viewing its contents To select and highlight an existing group access the Table Groups control panel as under Creating a named group from a selec tion Select the name of that group by clicking its name in the Groups In Table list box Click the SELECT pushbutton If you want only the desired named group to be visible in the table window please see Viewing named groups Please see the on screen help for details on the functioning of each control in the Table Groups control panel Deleting a group definition Removing named groups Removing all groups Additional information You can delete a group definition from the current table This deletes only the definition not the rows and or columns them selves which remain in the table To remove the definition of an existing group access the Table Groups control panel as under Creating a named group from a selec tion Select the name of that group by clicking its name in the Groups In Table list box Click the DELETE pushbutton To remove all group definitions from the table click the Delete All Groups act
329. n ascending order according to the model ID number These numbers are assigned serially as new model spaces are created They cannot be reas Cerius Modeling Environment April 1999 205 6 Managing Modelsand Sessions signed during the current session and are not reused if a model space is deleted The current diamond tool Place the current model at the top of the model table and sort all other models in ascending order by model ID number The name tool Sort model table entries alphabetically by name The visibility tool Place all explicitly visible models at the top of the model table sorted in ascending order by model ID number followed by the current model if it is not explicitly visible followed by all invisible models sorted in ascending order by model ID number Moving models between model spaces Finding information This section includes information on Copying whole models from one model space to another Moving parts of models from one model space to another Copying models to and from other applications Copying whole models from one model space to another Copying to the current model space You can copy the contents of some other model space to the cur rent model space You can copy a model into an empty current model space for example to use it as a base for additional building operations You can also copy a model into a current space that already con tains a model so as to
330. n change which atoms are cur rently selected for specifying each definition If symmetry constraints do not allow the requested translation it is not performed Please see the on screen help for details on the functioning of each control in the Position Atoms control panel You can position atoms while adding them to a model with the Add Atom control panel see Precise positioning of atoms during building Cerius Modeling Environment April 1999 177 5 Building Models Refining the conformation Cleaning the structure Additional optimization The model structure as initially drawn is usually not chemically reasonable Thus it needs to be cleaned i e its structure needs to be optimized Initial optimization is often done with the CLEAN button in the Sketcher control panel Simply click the CLEAN button and keep the left mouse button depressed until the structure in the model window stops changing You can adjust how the clean function works please see Control of the model cleaning function You may adjust the structure as desired after you clean it e g Examining and changing bond lengths However a better approach may be to apply constraints before additional optimization or to apply symmetry next paragraph If you want an even more chemically correct structure than the clean function is capable of you may want to use a forcefield based minimizer such as the OFF Minimizer or optimize the struc
331. n modules running on external servers Cerius applications are implemented as modules that plug into the modeling environment provided by the Visualizer Most Cerius application modules function either individually or grouped with related modules as independent processes As a result these application modules can be run on your local machine or externally on a remote host of the same or different type any where on your network This implementation method has several advantages including You can start and run only the application module s that you want to use thereby saving memory and reducing overhead You can purchase licenses to run application modules only on certain machines and still control those modules from any other machine on your network You can run application modules that perform complex com putationally intensive calculations on remote servers which may be more powerful than your own local machine To run application modules externally you use the controls on the Process Management control panel to select the appropriate appli cation module process remote host and executable program to modify any of your selections if necessary and to specify that the module should be started either immediately or when the module is accessed from a menu card Once you have started an applica tion module on a remote host you can also use the Process Man agement control panel to stop that module s process
332. n the screen Moving the cursor up and or to the right increases the magnifica tion moving it down and or to the left decreases magnification To shrink or expand the view so that the models almost fill their model window pane s you can do any of Select the View Fill Window menu item in the main control panel Press lt End gt on an extended keyboard Press lt Alt gt w on your keyboard Select the View Orient menu item to access the Orient View control panel Click the FILL WINDOW pushbutton To obtain the largest viewing area possible you can change the size of the model window To enlarge the model window so that it fills the computer screen you can do any of Press lt F2 gt on your keyboard Select the View Options menu item to access the View Options control panel Click the Set to Full Screen action but ton Grab a corner of the model window and pull it to the desired size To return the model window to its usual size you can Press lt F2 gt on your keyboard or Click the Reset to Default action button in the View Options control panel To change the view scaling of the models in increments you can place the cursor in the model window and Press lt gt or lt gt on an extended keyboard or Select the View Dials menu item to access the Viewing Dials control panel Cerius Modeling Environment April 1999 235 8 Viewing and Displaying Models Conti
333. n the x y plane 24 Cerius Modeling Environment April 1999 What you can do with a model display 16 Zooming in or out on a model You can control the magnification of the view of your model With the cursor in the model window hold down the middle and right mouse buttons Moving the cursor up and or to the right increases the mag nification Moving the cursor down and or to the left decreases the mag nification Keyboard shortcut If you have an extended keyboard pressing the and keys on the keypad increases and decreases the magnification 17 Returning the model to the center of the model window Click the reset tool on the toolbar to reset your model to its ini tial position The reset tool looks like Keyboard shortcut lt Home gt on an extended keyboard also resets the view 18 Selecting atoms Definition Sometimes you will need to perform activities on only certain atoms not on the entire model For this purpose you select atoms You can select them one at a time Click any atom to select it Cerius Modeling Environment April1999 25 2 Introducing C erius A beep confirms that you ve succeeded and the atom is highlighted to indicate that it is selected Click another atom to select only it Hold down lt Shift gt and click one or more atoms to select addi tional atoms lt Shift gt click an already selected atom to deselect it Click any on
334. n turn off global ambient lighting by setting Gray to 0 0 in the Lighting control panel You can turn off any numbered light by choosing it from the Light popup in the Lighting control panel and unchecking the Enabled check box A tutorial example of using the lighting controls to illuminate a model is found under Lighting your model Please see the on screen help for details on the functioning of each control in the control panels mentioned in this section Adjusting global light settings Two sided lighting Viewing position Ambient light To light both the inside and outside of models displayed in cylin der style Bonds as cylinders or both sides of solid surfaces e g such as those produced with one of the quantum chemistry mod ules check the Two Sided Lighting check box This control has no effect with ball or ball and stick display styles To change your virtual viewing position check or uncheck the Local Viewer check box Depending on the type of model display style and light position s the model may or may not look better with local viewing However graphics speed can be noticeably slower with Local Viewer enabled To change the brightness of the ambient light adjust the Gray con trol This affects only the global ambient light which does not have any discrete light source To use a colored ambient light use the red green and blue sliders or the entry boxes below them to set the proportions of red
335. nctions 0 0c eee 49 Before you begin 0 6c eee eee 50 Step by step tutorial 0 0 cece eee 50 A Loading and displaying a molecular model 50 B Viewing and labeling a model 53 C Selecting atomS nannan cee eee 55 D Manipulating control panels 57 REVICW ie et araa fates EE A le AET a arpa alate ER E 61 Related material n nnna nannan nna 62 Using the 3D Sketcher 0 6 cece 62 Before you begin 0 6c eee 63 Step by step tutorial 6 6 6c 64 Cerius Modeling Environment April1999 v A Building cyclohexane and saving the structure to file 64 B Converting cyclohexane into the boat conformation 68 C Editing cyclohexane to make benzene 69 D Editing benzene to make phenol 71 E Building xylene from template fragments 74 REVIEW A a otent anit n opcode rash Dae eee Lay Ree a 75 Managing Models and More 1 0 00 0 eee eee 76 Before you begin 6 cee eee 77 Step by step tutorial 6 eee 77 A Using the model manager 0005 78 B Making picric acid from phenol transferring data between model spaces 0000 000s 82 C Building a model of indigo 84 D Measuring the indigo model 86 E Generating hard copy 6 cece eee eee 88 Reviews A wh uan dea Alii aes Say death aa a A whdeard dh ane 92 Related material 2 0 0 0 ccc ee ee 92 Managing and Modifying Graphs s s sa
336. nd Administration Guide Select the Utilities Customize Environment menu item in the main Visualizer control panel to access the Customize Environ ment control panel This control panel is used in many of the tasks mentioned in this section Most window managers allow frequently used applications to be configured as desktop or tool box icons or as popup menu items for easy launching If you want to use one of these methods you need to configure the launch action so that the cerius2 script is invoked from a shell win dow The startup shell window becomes the text window to which Cerius sends certain information To learn the application launching shortcuts supported by your window manager and how to configure them please refer to that window manager s documentation You can suppress the display of the Cerius startup banner also called a splash screen if you want by using the nobanner option when you start Cerius for example gt cerius2 nobanner Generally Cerius runs by default in either OpenGL or GL graph ics mode as appropriate to your machine If your machine is capa ble of running in either mode and you want to force it to run in the nondefault mode you can set the FORCEOPENGL or FORCEGL env to any value before starting Cerius For example gt setenv FORCEOPENGL 1 or gt setenv FORCEGL 1 396 Cerius Modeling Environment April 1999 Balloon help Adjusting the beeper Finding atom in
337. nd rows can be referenced by their labels in expressions For example column velocity column time Index The sequence number of a row or column assigned by Cerius Columns or rows can be referenced by their index numbers in mathematical expressions For example column 2 column 3 To reference the current row or column in an expression use row and col The type of data that cells can contain is generally assigned to all cells in a column Cells in tables generated by Cerius application modules may be weakly or strongly typed Weekly typed columns Regardless of the data type specified for a column its cells can contain data of any type 334 Cerius Modeling Environment April 1999 Accessing the tools Entering mathematical expressions Valuesand mathematical expressions Strongly typed columns Some Cerius application modules create strongly typed columns Cells in these columns can con tain only the type of data specified for the column Generally you cannot enter data of another type into a strongly typed cell For example if a strongly typed cell is assigned the character data type you cannot enter numbers into the cell However Cerius can convert some data into the appropriate type For example if a strongly typed cell is assigned the inte ger data type and you enter a value of 2 2 Cerius rounds the value to 2 and stores it as an integer How to change the data type where possible is
338. need hints on how to do this refer to the Basic GUI Functions tutorial lesson Reset the view use the f icon beside the label popup on the tool bar Cerius Modeling Environment April 1999 67 3 Tutorials 6 Save the cyclohexane model into a structure file Select File Save Model to open the Save Model control panel Type cyclohexane msi into the filename text box which is next to the Save button then select the Save button to save the structure to a file Use the directory selector popup and the file browser on the panel to find the correct directory before you save the file B Converting cyclohexane into the boat conformation In the following steps you learn how to move atoms to convert the chair conformer of cyclohexane into the boat conformer 1 Adjust your view of the model Use the mouse to rotate the model to view the chair from the side Select the carbon on one end of the ring as you look at it and select the two hydrogens attached to that carbon Remember you need to hold down the lt Shift gt key to select multiple 68 Cerius Modeling Environment April 1999 Using the 3D Sketcher atoms Hold down the lt Control gt key and drag with the middle mouse button to move the selected atoms Drag these atoms well to the other side of the plane defined by the four car bons in the seat of the chair Clean the model
339. nel to Additional Graph Open the Load Graphs control panel File gt Load from the Graphs card and load the file Cerius2 Resources EXAM PLES data EM_PM_Emix grf There are now two Emix Fit graphs listed in the Graph Chooser list box and two Emix Fit graphs on display in the graph window 4 Delete the second graph On the Gallery Manager control panel set the second ver sion of the Emix Fit graph to off Then choose the CLEAR button of the Graphs Expert Functions control panel This deletes the second version of the Emix Fit graph 5 Combine the data sets from the two graphs Set the Data Placement option to Combine With Existing Re load the Cerius2 Resources EXAMPLES data EM_ PM_Emix grf graph file This time when you load the second version of the Emix Fit graph the data sets from the two versions are combined and displayed on the same Cerius Modeling Environment April 1999 113 3 Tutorials axes a Fis 3C sixiu Puviyy Now set the Data Placement popup to Replace Existing and reload the Cerius2 Resources EXAMPLES data EM_ PM_Emix grf Now the older version of the graph is overwritten by the new one Replace Existing is the default for Data Placement when a compu tational module creates versions of the same graph the Replace Exist ing option prevents these many obsolete versions from accumulating in the gallery 6 Make two graphs with identical axes Op
340. ng control Rendering and ray tracing Stereo viewing Important P To exploit Cerius s graphics functionalities to the full you need to be running it on a machine with sufficient memory and graphics display capability Some of the effects discussed in this section may appear less dramatic on lower end machines Table 8 Finding information about enhancing model display If you want to know about Read Changing colorof selected atoms Coloring selected objects Changing colorofallatomsofan element Default element colors Coloring atomsaccording to othercharac Coloring atoms by properties teristic s Mapping atomic properties to colors Property color mapping Changing the background color Background color in model window Cerius Modeling Environment April 1999 263 9 Enhancing Model Display Table 8 Finding information about enhancing model display If you wantto know about Read Changes colors used by the Cerus inter Interface colors face Illuminating models from defined directions Directional lights Spotlighting parts of models Spotlights Labeling and annotating models Labeling and annotating models Changing the display resolution Resolution and graphical quality Printing models Printing models and graphs Exporting to non C erius applications Copying models to and from other applications Saving preferences Using saved sessions as preferences settings You should already The basics
341. ng graph appearance Adding labels amows etc Editing graph axes Shifting scrolling orzooming an axis Mouse buttons and keyboard use Starting to edit how data setsare dis played Read Accessing the tools Concepts Selecting graphs to display Preventing replacement of old graphs Graphing table information Selecting graphs for editing Changing plotting style and color Labeling and annotating graphs Changing graph axes and scale Changing graph axes and scale Mouse and Keyboard Actions Selecting a data set Cerus Modeling Environment April 1999 291 10 Working with Graphs Table 10 Finding information about graphs If you want to know about Read Displaying or hiding data sets Colorrangesin 2D graphs Selecting a data set Specifying color use in 2D graphs Changing colorranges used in graphs Color ranges Setting graph preferences Printing graphs Controlling default display format Printing models and graphs Saving files containing graphs Saving graphs Saving individual models Saving graph and other preferences Using saved sessions as preferences settings Loading files containing graphs Loading graphs Loading model structure files Finding files with file browsers in control Loading model structure files panels Formats of graph files Freeing memory and clearing graph display You should already know Accessing the tools File Formats the Removing graphs and
342. ng individual atoms are demonstrated under Selecting atoms Related information You can also select atoms in several models simultaneously Select ing atoms in several models Selecting and deselecting individual atoms The mouse is in selection mode when the selection tool in the Sketcher control panel is highlighted In addition the cursor is shaped like an arrow pointing to the upper left when it is in the model window This tool is also found in other control panels and selection is always the default mode You always use the left mouse button to select atoms in the model window Single atom picking To select only one atom simply click it A beep confirms that you ve succeeded and the atom becomes highlighted To select only one different atom click it Cerius Modeling Environment April 1999 159 5 Building Models Using a selection rectan gle Operating on all atoms Tip To select additional atoms keep lt Shift gt depressed and click the appropriate atoms in other words lt Shift gt click them To deselect some but not all selected atoms lt Shift gt click them To select only all atoms in some area of the model window click nearby and drag out a selection rectangle that encloses the desired atoms The atoms must be visible to be selected see Visibility of polymer backbones To add all atoms in another area of the model window to the selection lt Shift gt drag a selecti
343. ng longitude from 360 if it is greater than 180 since the value entered must be lt 180 You may also want to increase the Radius of the spotlight s position using the Lightsource Position control panel to illuminate the entire model Final adjustments Then you can narrow the cutoff and iterate using the Cutoff and Spotlight Direction controls in the Spotlight Settings control panel as well as the position controls in the Lightsource Position control panel until the light shines exactly where you want it 286 Cerius Modeling Environment April 1999 Rendering and ray tracing To make the illuminated area gradually fade into the nonillumi nated area of your model you can increase the Falloff value Larger values make the light relatively more intense near the cen ter of the light cone and smooth the transition from the light to the dark area Related information If the edges of the illuminated area appear too jagged you can increase the display resolution see Object resolution Light attenuation Positional lights Positional lights whether or not they are also spotlights Spotlights can be attenuated to make objects that are closer to the light source appear brighter than those farther away Concepts Accessing the tools Click the Attenuation pushbutton in the Lighting control panel to access the Lightsource Attenuation control panel Adjusting the attenuation To make the relative brightness a linear functi
344. nor an acceptor The hydrogen bonding nature of elements can also be changed with the Edit Elements control panel see Element properties When these criteria are altered any existing hydrogen bonds that no longer meet the criteria are deleted when you click the CALCU LATE pushbutton in the Edit Hydrogen Bonding control panel Hydrogen bond recalculation occurs automatically if the Enable automatic recalculation check box in the Edit Hydrogen Bonding control panel is checked Please see the on screen help for details on the functioning of each control in the H Bond Calculation Preferences control panel To request hydrogen bond calculation between all or selected atom pairs that meet the criteria click the CALCULATE pushbutton in the Edit Hydrogen Bonding control panel Inttoduc ing substitutional disorder Uses of substitutional disor Substitutional disorder can be used whenever two elements need der How it works to be randomly replaced in a structure For example substitutional disorder is particularly useful in dealing with zeolites where you may want to randomly replace silicon atoms with aluminum Substitutional disorder randomly replaces a fraction of the atoms of one element type with atoms of another element type Substitu tional disorder can be applied to the whole model or to only a selected portion of the model A target ratio is used to set the frac tion of the atoms to be replaced Lowenstein s rule appli
345. ns You can align cell content in selected column s or the current cell both vertically and horizontally As with many functions in the Table Properties control panel alignment does not work on selected rows if you select a row only the current cell in that row is aligned as specified Accessing the tools To modify any table properties you need to access the Table Prop erties control panel Click the PROPS tool in the table manager tool bar or Select the Data Properties menu item from the TABLES card To align the contents of selected columns or of the whole table access the Alignment pane of the Table Properties control panel by setting the Properties popup to Alignment Aligning selected columns Assure that the Selection control is selected select the desired or the current cell Horizontal and Vertical alignments and click the APPLY TO pushbutton The contents of the selected column s or of the cur rent cell if no column is selected are aligned as specified 328 Cerius Modeling Environment April 1999 Aligning the entire table Aligning named groups Additional information Table style and display Assure that the Entire Table control is selected select the desired Horizontal and Vertical alignments and click the APPLY TO pushbutton The contents of all columns in the table are aligned as specified Columns within named groups Grouping table information can similarly be alligned by selecting th
346. ns 384 overwriting 210 spac 425 panels 394 PDB 426 pdb 426 POLYGRAF 419 PostScript 258 259 288 PSYCHO input 288 QUANTA 418 ray tracing 288 289 related projects 209 res 427 RUN LOG 377 saving 210 segment log file 377 selecting 198 session 213 SHELX 427 specifying 197 supplementary log file 377 supported formats 415 tbl 296 297 319 327 416 temperature factors 427 trajectory 241 trj 241 xtl 419 xy 297 434 xyz 425 Z matrix 425 Find Cells control panel 355 357 359 361 FORMAL CHARGE 243 fractional bond order 244 fragment tool 9 fragment definition 161 fragments connecting 157 fusing 156 loading 14 moving one but not others 41 Frame Filter control panel 241 242 function keys 407 Fuse tool 156 fuse definition 156 G Gallery Manager control panel 294 298 299 301 Graph Annotation control panel 300 301 Graph Manager control panel 295 296 299 Graph Scaling control panel 301 302 303 graph window 297 298 clearing 308 309 proportions 301 302 updating 298 width and height 298 graphics contrast 284 drawing speed 258 lighting 279 mono 290 perceived three dimensionality 285 289 quality 258 259 287 ray tracing 287 rendering 287 Cerius Modeling Environment April 1999 441 resolution 258 smoothness 258 specularity 258 stereo 289 graphs 291 304 2D Cartesian 294 2D polar 294 adding data 295 299 307 308 angle between axes 301 302 angles in
347. nt You can specify the resolution in dots per inch for curves in graphs Increasing this value allows improved definition of these images although the resolution of the output device is always a limiting factor Increasing the resolution results increases the Post Script image generation time file size and printing time If yourun Cerius on an SGI platform you can click the PREVIEW pushbutton in the Print control panel This calls up SGI s xpsview utility to preview your PostScript image before sending it to the printer or a file Once all options have been set to your satisfaction click the PRINT pushbutton in the Print control panel A tutorial example of printing a model is found under Printing a model Please see the on screen help for details on the functioning of each control in the Print and Page Setup control panels Changing the resolution with which graphics are displayed and written is cov ered under Resolution and graphical quality Cerius Modeling Environment April 1999 261 8 Viewing and Displaying Models 262 Cerius Modeling Environment April 1999 Enhancing Model Display The Cerius e Visualizer includes many facilities for enhancing the display of your model enabling you to interpret it better and to prepare effective graphical output This section explains This section contains information on Model display colors Customizing display colors Surfaces style and transparency Lighti
348. nt color 179 265 default color 265 editing 16 166 265 hydrogen bonding nature 179 184 ionicity 179 mass 179 properties 179 radii 179 182 random replacement 184 saving 210 specifying during building 151 Element Mixtures control panel 180 element name 180 element symbol 180 ELEMENTS 243 enter definition 14 entry boxes 140 erasing a model 13 examples pre recorded 46 exchanging data with non Cerius2 databases or applications 211 Export Table control panel 365 366 F ferrocene 32 FFYTPE 243 file text output 382 file browser example illustration 197 using 197 file formats grd 370 mbk 370 Cerius2 structure files 415 FDAT 415 isosurfaces 370 MSF 418 filename filters 197 files applcomm db 387 arc 415 ASCII for tables 319 BGF 419 bgf 419 BIOGRAF 419 C2Psycho dat 288 C2Psycho eps 288 C2Psycho ps 288 Cambridge 421 car 415 cerius2 ini 381 CHARMm 418 con 297 434 cor 415 CSSR 423 cssr 423 440 Cerius Modeling Environment April 1999 dat 320 decks 391 dot 225 exported tables 366 fcssr 423 FDAT 421 fdat 421 finding 197 formats 197 199 210 211 415 graphs 297 309 428 grf 296 297 309 428 gui_colors 395 ICSD 424 icsd 424 loading 198 loading several 198 log 377 MACCS Molfile 424 master par 425 mdf 415 model structures 415 mol 424 MolEN 425 MOPAC 425 msf 418 MSI 416 msi 21 211 416 MSI format 211 mss 213 naming 210 NMRegraf 419 old 434 optio
349. nter of the arrow tools or press lt Home gt on the keyboard You can also scroll graphs interactively by placing the cursor within a graph depressing the middle mouse button and drag ging the mouse in any direction within the xy plane The proportions rectangular or square of all types graphs can be changed In addition the x and y axes of x y graphs can be expanded or contracted zoomed see Expanding or shrinking an axis To change the proportions of the Cerius2 Graphs window and any graph s it contains grab a corner of the window with the cursor 302 Cerius Modeling Environment April 1999 Expanding or shrinking an axis Additional information Displaying and editing graphs and drag it Changing the graph window s width and height Accommodating graphs within the graph window also affects the pro portions of the displayed graphs Alternatively you can set the window proportions by entering a number in the Aspect ratio entry box in the Gallery Manager con trol panel To zoom in on a specific part of the displayed graph hold down lt Alt gt and the middle mouse button and drag out a rectangle over the desired part of the graph To expand the graph along the x or y axis use the tools in the Zoom controls of the Graph Scaling control panel To contract the graph along the x or y axis use the tools in the Zoom controls of the Graph Scaling control panel To return the view to its original positi
350. ntrol panel Background color in model window Accessing the tools Changing the back ground color Tip Additional information You may want to change the background color in the model win dow to enhance the appearance of the model or because you may require a light background To change the color of the model window background from the default black to something else select the Utilities Customize Pen Colors menu item to access the Pen Colors control panel To change the background to white black or one of two shades of grey choose the desired color from the Background popup To change the background to any color either set the Pen popup to BACKGROUND or set the Background popup to OTHER Then use the red green and blue sliders or the entry boxes below them to set the proportions of red green and blue desired in the back ground color To improve the appearance of your model after you change the background color or to for example enable hydrogens to be seen against a white background you can use the lighting controls Lighting control and or change selected object colors Coloring selected objects or default element colors Default element colors Please see the on screen help for details on the functioning of each control in the Pen Colors control panel Customizing display colors Cerius provides several ways of customizing the use of colors in the model window 268 Cerius Modeling Envi
351. nts control panel Distances To change the length of a bond precisely select the Move Bond Geometry menu item to access the Bond Geometry control panel Please see the on screen help for details on using the controls in the Bond Geometry control panel to measure and change bond lengths valence angles and torsions and to specify which atoms are moved in the process You can also modify bond lengths by translating Translating atoms precisely or positioning Aligning and positioning atoms atoms to specified locations You can also examine bond lengths and other distances with the Measurements control panel Distances You can change the defaults that Cerius uses in calculating bonds To change the default radii of atoms please see Element properties For covalent bond calculation preferences see Bond properties For setting the hydrogen bond length criterion see Hydrogen bonds Examining and changing angles Important Changing an angle man ually Cleaning a structure Refining the conformation automatically optimizes all valence angles You can change angles before cleaning if you want to bias the final structure However if you want a different specific angle than that determined automatically change it after using the clean function clean only selected atoms Control of the model cleaning function or do not use cleaning To change a valence angle manually select the Angle tool in the Sketcher control pan
352. nuous zooms Precise magnification Additional information To zoom into or out of the models use the arrow tools in the Magnification controls To return the models to their original magnification click the reset button between the arrow tools Select the View Dials menu item to access the Viewing Dials control panel Click and hold one of the Magnification arrow tools Select the View Dials menu item to access the Viewing Dials control panel Enter a value in the Magnification entry box Values greater than 1 0 enlarge the display Values less than 1 0 shrink the display Please see the on screen help for details on the functioning of each control mentioned here Mouse functions and keyboard shortcuts are summarized in Mouse and Keyboard Actions Setting position and orientation Resetting the view Topics in this section include resetting the view of the models to the default position orientation and magnification centering the display the differences between centering and resetting are pre sented in this section and defining a center of rotation for the cur rent model Resetting changes the viewing angle so that the model s x y and z axes are coincident with the window x y and z axes Any transla tions are reversed by returning the model to the origin and the magnification is returned to unity To reset the view of the models you can do any of Click the reset tool on the toolbar Selec
353. nvironment April 1999 Managing and Modifying Graphs Change the popup options from Yes to No and back again so you can identify the various components of the graph Axes Label Title and Key The Cell option only applies to 3D graphs Note You will never want to select gt because it has no effect However Cerius may set a popup to gt to indicate that this option is not unique for the graphs in the edit list Edit the X Axis Label the Y Axis Label and Graph Title text boxes Notice that the text on the graph is updated with the new labels and Cerius Modeling Environment April 1999 107 3 Tutorials E Saving graph files title SORPTION Loading Plotvl Annotation Options Axes Labels Tite Key Cell YES x Axis Label External Pressure Pa y Axis Label Sorbate loading unit cell Graph Title Practice Graph difor tutorial exercise Close the Graph Annotation control panel A graph grf file can contain a single graph or multiple graphs Each of the graph files that you loaded in section A page 96 con tained only one graph In the following steps you save a gallery of two graphs into one grf file Then you reset the Graphs card and load back in the two graph file that you saved 1 Save multiple graphs into one file On the Gallery Manager control panel select the Emix Fit and the Thermodynamics graphs to be displayed and do not
354. o adjust the points at which depth cueing takes effect The adjustments take effect immediately and are more easily seen at lower values of the depth cue factor Since caffeine is a nearly planar model you can see the effects of depth cueing more readily by turning it so that it is no longer parallel to the computer screen 36 Lighting your model Lighting effects are more dramatic if you have a model with some solidity so Change the display style to BALL Select the View Graphics Lighting menu item The Lighting control panel appears You can experiment with the con trols on and accessible from this panel Remember you can click with the right mouse button to obtain help on any control You can for example Change the color of the global ambient light by adjusting the Color sliders in the Lighting control panel Make it a rather dim neutral color so that you can more easily see the effects as Cerius Modeling Environment April1999 43 2 Introducing Cerius you add light sources More lights You can even turn it off by setting Gray to 0 0 Click the Color button to access the Lightsource Colors con trol panel where you can change the colors and brightness of the various components of LIGHT 1 If nothing happens If some of these controls appear to have no effect you are probably not running Cerius in OpenGL mode see Important Click the Position button in the Lighting control
355. o save models relating to a specific project together or save related models as a database To do so go to a UNIX shell window not the one from which you are currently running Cerius cd to the desired parent directory and create your subdirectory with the UNIX mkdir command This can be done at any time For example gt ed CeriusRuns Cerius Modeling Environment April 1999 209 6 Managing Modelsand Sessions Saving the current model Example Additional controls Saving part of a model Additional information What is saved as a model gt mkdir myModels Alternatively you can use the the text window and prefix a to the UNIX commands Text window Select the File Save Model menu item from the main control panel s menu bar to access the Save Model control panel This control panel is used to save the current Basic model management tasks model Use the file selector controls in the Save Model control panel to move through the file system to the directory in which you want to save the current model Newly created directories appear in the file selector list box when the appropriate parent directory is opened or reopened with the file selector controls or when the con trol panel is opened After selecting the appropriate directory specify a name for the structure file by typing that name in the file name entry box then press lt Enter gt or click the SAVE button A warning helps prevent y
356. o specify the type of graph choose Line ScatterPlot or Histo gram from the Type popup If you want a title for your graph enter it in the Title entry box You can enter axis labels for the x and y axes in the Axis Label entry boxes on the right and left sides respectively of the control panel Finally click the PLOT pushbutton in the Plot Table control panel 364 Cerius Modeling Environment April 1999 Note Additional information Exporting table information Additional control over graph style range labels annotations etc is available in the Graph module of Cerius Working with Graphs and can be used to modify graphs after they are generated by the Table module and to control for example whether new graphs replace or are added to previous graphs displayed in the graph window The graph in the graph window is not automatically updated if you change the data in the table or decide you want a different type of graph You must click the PLOT pushbutton to regenerate a graph Please see the on screen help for details on the functioning of each control in the Plot Table control panel Exporting table information Related information You should already know Accessing the tools You can export all or part of the current table to disk in a variety of formats for later importation into an external program such as a spreadsheet The usual procedure for saving a table in the default MSI table for m
357. oad the session file before building or loading any models Related information Information on controlling Cerius from prerecorded command scripts is given in Controlling Cerius2 from scripts Other customization activities are covered in Customizing the Inter face Cerus Modeling Environment April 1999 215 6 Managing Modelsand Sessions 216 Cerius Modeling Environment April 1999 Geometry Analysis The Visualizer s analysis and evaluation tools enable you to closely examine the three dimensional structure of the models you are studying This section explains This section contains information on Measuring models Calculating close contacts Model surfaces Vector properties Related information Some other Cerius application modules also contain various types of functionality for analyzing model geometry or calculating other types of surfaces Information on using these tools is found in the specific documentation for the relevant application mod ules Table 5 Finding information about geometry analysis of models If you wantto know about Read Measuring distances angles torsions and inver Measuring models sions of models Examining and changing the model s geometry Editing the structure Refining the model s conformation Refining the conformation Close contacts between nonbonded atoms Calculating close contacts Solvent accessible surfaces formodelsof a mole Model surfaces cule surface or
358. of starting Cerius and using its interface are demon know strated in Introducing Cerius2 and described in The Cerius2 Interface You need to know how to build Basic building and or load Load ing model structure files models You should know how to select atoms in model s Selecting atoms and groups of atoms and how to position models on the screen Moving models on the screen If your session contains several models you should know how to specify the current model Specifying the current model or select atoms in more than one model simultaneously Selecting atoms in several models Model display colors Cerius provides several methods of changing the colors of atoms according to their element type and other properties Finding information This section includes information on Default element colors Coloring selected objects Coloring atoms by properties Background color in model window 264 Cerius Modeling Environment April 1999 Related information Model display colors Displaying labels and other information about atoms in a model is presented under Labels Saving nondefault settings for later use is described under Working with Cerius2 sessions Default element colors Accessing the tools Changing element default colors Example Additional information To help in understanding models atoms are colored according to their element For example carbon is dark grey hydrogen is white and oxygen i
359. ol bar Panels This stacks all the open control panels with their title bars visible Lone Atom Style Highlight Mul iple Bonds Ball Size Cylinder Cylinder Radius A Ball amp Stick Ball Size Stick Radius 4 Ellipsoid S ze Show Principal Axes Show Bonding Polyhedra Non Polynedral Style Resolution Spheres CO Jw Ellipsoids CTs J Line Widta fn X PostScr pt Qualizy Bring the last panel to the front by clicking on its title bar and close it by selecting its close box in the top right cor ner 60 Cerius Modeling Environment April 1999 val Clear Panels 6 Te Basic GUI Functions Close the control panels Select the Clear Panels button on the tool bar The remaining control panels close If you are going to continue immediately with another tutorial Re initialize the program by selecting File New Session and selecting the Confirm button on the Re initialize dia log box Re initialization resets all the Cerius control panels to their original defaults Alternatively if you want to stop now Choose File Exit to quit from Cerius and select the Exit button on the Exit Option dialog box Review In this tutorial you learned how to gt e e gt oe Oo Load an msi structure file Change the display style of all or some atoms Rotate translate and scale the model view in the model window
360. ol panel as under Creating a named group from a selection Enter aname for the new group in the Group Name entry box Select the Group tool and enter the name of the first group to be merged in the Group entry box by choosing its name from the associated popup Click the CREATE pushbutton The new group s name appears in the Groups In Table list box and should be highlighted Enter the name of the second group to be merged in the Group entry box by choosing its name from the associated popup and click the MERGE pushbutton Repeat for any additional groups that you want to include in the new group To simply merge the contents of two or more existing groups with out creating a new group access the Table Groups control panel as under Creating a named group from a selection Select the name of the group that you want to add material to by clicking its name in the Groups In Table list box Select the Group tool and enter the name of the group to be merged in the Group entry box by choosing its name from the associated popup Click the MERGE pushbutton Repeat for any additional groups that you want to include in the enlarged group To remove selected rows and or columns from an existing group access the Table Groups control panel as under Creating a named group from a selection Select the name of that group by clicking its Cerius Modeling Environment April 1999 355 11 Working with Tables Additional information name in the Groups I
361. oms are displayed select the View Display Attributes menu item to access the Display Attributes control panel Click the Preferences button to access the Style Prefer ences control panel In the latter control panel set Lone Atom Style to CROSS BALL POINT or NONE Atoms can be represented by space filling balls If any bonds are visible between balls they are represented as lines To display atoms in ball style you can Set the display style popup on the toolbar to BALL or Select the View Display Attributes menu item to access the Display Attributes control panel Set the Style popup to BALL The ball radii are proportional to the van der Waals radius of the respective atoms To set the ratio of ball radius to van der Waals radius click the Preferences pushbutton in the Display Attributes control panel to access the Style Preferences control panel Enter the desired proportion in the Ball Ball Size entry box Ball and stick style represents atoms as van der Waals spheres and by bonds as cylinders 252 Cerius Modeling Environment April 1999 Specifying ball and stick style Setting the ball radii Setting the stick radius Cations as polyhedra Understanding the display Specifying polyhearal style Model display style X To display models in ball and stick style you can Set the display style popup on the toolbar to BALL amp STICK or Select the View Display Attributes menu
362. on except that rotation continues when you release the mouse button To stop the movement move the cursor out of the model window press lt Esc gt on your keyboard or click the right mouse button anywhere in the model window ROCK As for CONTINUOUS except that rotation occurs only through the angle specified in the associated entry box The direction of rotation alternates so that the model view rocks To stop the movement move the cursor out of the model window press lt Esc gt on your keyboard or click the right mouse button anywhere in the model window To quickly change the viewing angle in large steps place the cur sor in the model window and then To rotate the models by 45 about the x axis press the up or down arrows on an extended keyboard Cerius Modeling Environment April 1999 233 8 Viewing and Displaying Models Continuous rotation Precise rotation Orienting according to atom positions Additional information To rotate the models by 45 about the y axis press the right or left arrows on an extended keyboard Select the View Dials menu item to access the Viewing Dials control panel To continuously rotate the models about the x y or z axis click and hold a slider or click and continuously drag a dial pointer Select the View Dials menu item to access the Viewing Dials control panel To rotate the models to a specific angle about the x y or z axis drag the sliders clic
363. on that is to the same mag nification as before you began zooming click the reset button in the center of the Zoom tools or press lt Home gt on the keyboard You can also zoom graphs interactively by placing the cursor within a graph and Holding down the middle and right mouse buttons and drag ging the cursor in the model window or Holding down lt Shift gt plus the middle mouse button and dragging the cursor in the model window Moving the cursor up and or to the right increases the magnifica tion along the y and or x axes respectively moving it down and or to the left decreases the magnification Please see the on screen help for details on the functioning of each control in the control panels mentioned in this section Mouse functions and keyboard shortcuts are summarized in Mouse and Keyboard Actions Changing plotting style and color You can change features of the graph appearance such as style and color For 2D graphs you can also set whether data values are dif Cerius Modeling Environment April 1999 303 10 Working with Graphs Related information Accessing the tools Changing line style and color in x y graphs Changing the style of 2D graphs Specifying color use in 2D graphs ferentiated by lines of constant value contours or by spots or areas of color and also specify how colors are applied Selecting graphs Selecting and displaying graphs and data sets Selecting whic
364. on module The contents in them selves are irrelevant for this tutorial and you needn t have licensed the Blends or the Sorption modules to load or manipulate these graphs 1 Load the graph files Find the Graphs card on the Tables amp Graphs card deck If the card is not already at the front of the deck click on the card title to bring it to the front 96 Cerius Modeling Environment April 1999 Managing and Modifying Graphs Open the Load Graphs control panel by choosing the File gt Load Graphs item on the Graphs card Find the directory Cerius2 Resources EXAMPLES data Be sure that the filename text box at the bottom of the browser box reads gif Load the file EM_MM_DG grf pick its name on the browser box and then click the Load button A confirmation message like the one shown below appears in the text window The graph appears in the graph window Loading Grapher file Cerius2 Resources EXAMPLES data EM_MM_DG grf Loading Done Place the graph window in the top left corner of the screen over the Model window Enlarge the graph window click and drag a corner of the window until the window is almost as large as the Model window You do not need the Model window for this tutorial Now load two more graph files from the EXAMPLES data directory EM_MM_Emix grf and Loading grf Close the Load Graphs control panel Ce
365. on of the distance of an object from the light source enter a nonzero value for the Lin ear factor To make the relative brightness a square function of the distance of an object from the light source enter a nonzero value for the Qua dratic factor To uniformly make the illumination dimmer or brighter adjust the Constant control Rendering and ray tracing Cerius provides a rendering facilities that enable you to produce high quality 3D images of specified models and atoms Two ren dering facilities are provided RayTrace and PSYCHO PostScript utilitY for Color Hardcopy Output How RayTrace works Regardless of the display style that you have selected RayTrace uses the ball display style Atoms as balls and the currently defined default element colors to render atoms as van der Waals spheres The lighting controls Lighting control do not affect ray tracing at this time Cerius Modeling Environment April 1999 287 9 Enhancing Model Display How PSYCHO works Accessing the tools Rendering models The rendered image appears in a separate Cerius window called the Cerius2 Ray Tracing window The bitmapped image displayed in this window cannot be manipulated or printed However you can use a third party screen capture utility or print utility to cap ture or print the rendered image You can also save the intermedi ate files that are used in producing the ray traced image PSYCHO produces an encapsulated PostS
366. on rectangle around them To deselect a group of already selected atoms lt Shift gt drag a selection rectangle around them To select all atoms drag out a rectangle enclosing the entire model select the Edit Select All menu item press lt Alt gt a on the keyboard or click the select all tool see toolbar illustration at The controls For some functions selecting all atoms has the same effect as selecting none e g changing the display style Model display style or applying labels Labels Other functions e g deleting all atoms Deleting atoms and bonds require that all atoms actually be selected To deselect all atoms click in empty space in the model win dow or click the deselect all tool in the toolbar Selecting atoms in several models You should already know How it works You are not restricted to selecting atoms only in the current model Atoms in any number of displayed models can be selected This capability is useful for activities like monitoring close contacts between models Calculating close contacts and comparing models by superimposing them Superimposing models Managing and displaying multiple models is documented in Man aging Models and Sessions Selecting atoms works differently depending on how the models are displayed see Controlling model visibility and the display mode 160 Cerius Modeling Environment April 1999 Selecting atomsand groupsof atoms In over
367. on that Cerius always shows in the model window can be changed These functions are useful for understanding the displayed model and for enhancing the appearance of models for presentation and display purposes This section includes information on Labels Default annotation Custom annotations You can also enhance model displays by for example coloring atoms according to various properties Model display colors or color mapping properties onto model surfaces in for example the quantum chemical application modules which have separate documentation 242 Cerius Modeling Environment April 1999 Labeling and annotating models Labels Adding changing or removing labels on atoms Labels can be applied to entire models when all or no atoms are selected or to selected atoms within one or more models Different labels may be used for different parts of a model The following label properties are available NO LABEL No labels NUMBERS Atom serial numbers SYM NUM Crystal symmetry copy plus atom serial numbers ELEMENTS Element types CHARGES Atom partial charges FORMALCHARGE Atom formal charges OCCUPANCY Atom site occupancies ISOTROPIC Atom isotropic temperature factors FFYTPE Forcefield atom types HYBRID Atom hybridization NAME Atom name MASS Atom mass CHIRALITY Atom chirality To add change or remove labels on all or selected atoms you can Set the label popup on the toolbar to the desired property
368. onds command under the Build pulldown menu to view the predicted hydrogen bond ing 2 Calculate hydrogen bonds Select the Build Edit H bond from the top menu bar Click the Preferences button to see the criteria that will be used to judge the presence of hydrogen bonds Click the CALCU LATE button to display the pairs of atoms that fall within the H bond criteria Turn on the Enable Automated Recalculation so that the changing hydrogen bonding pattern will be displayed dur ing the molecular dynamics simulation Cerius Modeling Environment April 1999 123 3 Tutorials 3 Simulate the system dynamics Select the Dynamics Simulation card from the OFF METH ODS card deck and open the Dynamics Simulation menu by selecting Run This model is fairly small so the number of dynamics steps can be increased to 2000 without making the simulation too time consuming Each step simulates 0 001 ps so the entire run will simulate the behav ior of the glucose water system for 2 ps A certain amount of analysis is carried out during the simulation and results will be displayed in the graphics and graph windows but further analysis after the simulation completes requires data to be saved Select the Trajectory button at the bottom of the Dynamics Simulation menu or select Trajectory gt from the Dynam ics Simulation card to open the Dynamics Trajectory Out put menu Select to Create
369. ontrol on the TABLES card Cerius Modeling Environment April 1999 313 11 Working with Tables Introduction to Cerius tables Why read this section Finding information You should already know Additional information This section introduces basic features of the Table Manager win dow which controls the display of tables Since each part of this window is presented where relevant in the task oriented sections that follow Managing and editing tables this section is mainly use ful as an overview or if you don t have a table displayed on your screen This section includes information on The table window Keeping track of the current table How to access the Tables module is described under Accessing the tools Mouse functions and keyboard shortcuts are summarized in Mouse and Keyboard Actions Please see the on screen help for details on the functioning of each control in the Table Manager window The table window How it works Accessing the tools Any of several tables that are present in computer memory can be displayed one at a time in the table window The current table is selected with the table manager which is located near the bottom of the table window The current table then appears in the current table area of the table window where it may be edited and format ted etc Click the Show Table Manager menu item on the TABLES card to display the Table Manager or table window A new empt
370. ontrolling model visibility and the display mode and hiding any models you are not currently working with Controlling model visibility and the dis play mode should be most convenient however any display mode may be used Use any of the conventional means of defining a model as current Specifying the current model To translate the current model you can Press lt Shift gt and lt Ctrl gt on the keyboard and hold down the middle mouse button to move the cursor in the model window or Use the Translate Model controls in the Model Space Trans forms control panel to translate the current model along the x y or z display axis or along a user defined direction You can define a translation direction by entering a value in the Translate Rotate Axis entry box or selecting some atoms and then clicking the associated DEFINE pushbutton in the Model Space Transforms control panel The rotation axes are the display axes as shown in Figure 3 To rotate the current model you can Press lt Shift gt and lt Ctrl gt on the keyboard and hold down the right mouse button to move the cursor in the model window Move the cursor as described for simple rotation of all models Manual rotation or Use the Rotate Model controls in the Model Space Transforms control panel to rotate the current model around the x y or z 238 Cerius Modeling Environment April 1999 Specifying the center of rotation Saving the model
371. onvenience quickness and or accu racy The basic model viewing tools do not alter the original coordinates of the models They affect only the view and appearance of models in the model window Basic model viewing tasks affect all models and include Translating models Rotating models Changing the view magnification Setting position and orientation You rotate and translate models relative to the x y and z display window axes which are always oriented as shown in Figure 3 Cerius Modeling Environment April 1999 231 8 Viewing and Displaying Models These window axes are not the same as the model s viewing angle axes which are usually displayed in the lower right corner of the model window see Default annotation Figure 3 Window axes in Cerius model window The zaxis points perpendicularly out of the computer screen Example A tutorial example of basic model moving is found in Moving a model Translating models Manual translation To interactively translate models place the cursor in the model window and then press the middle mouse button and drag the mouse in any direction within the xy plane Incremental translation Select the View Dials menu item to access the Viewing Dials control panel 4 To move the models in an x or y direction use the arrow tools in gt the Pan controls hd To return the model to its original position click the reset button in the center of the arrow tools
372. operators 338 unary model operators 344 unary text operators 347 Measurements control panel 218 219 menu bar 8 function 133 illustration 134 menu cards 133 136 searching 142 menu items using 9 menus Build 145 Edit 145 Help 135 Move 145 View 231 message windows 143 metallic radius 179 mixture elements 180 model active 202 aligning 176 center of rotation 237 239 current 36 206 current defined 202 current specifying 202 current visibility 204 current where displayed 202 data 210 geometry measurement 27 hidden 36 ID number 203 labeling 23 fighting 43 magnification 25 movable 239 moving 24 45 moving relative to another model 237 name 36 205 new 201 printing 41 259 reference 239 renaming 205 resetting the view 25 rotating 24 slice 256 space 199 translating 24 viewing several 37 visible 37 zooming 25 model manager 133 model name 205 444 Cerius Modeling Environment April 1999 changing 205 selecting 203 selecting several 203 model space adding 32 39 201 clearing 39 202 deleting 39 202 selecting 203 Model Space Transforms control panel 238 239 model table 32 36 diamonds 36 202 example illustration 204 illustration 201 sorting models 205 squares 37 203 using 203 visibility indicators 203 model viewing controls 135 model window 128 axes 231 background color 268 changing the size 235 default annotation 244 models animating 242 annotating 245 appearance of depth 257 building 8 4
373. or respond to equivalent numbers in CONECT list Possible val uesare 1 0 and 1 17 DISPY DISPY 1X 1216 Y cell displacement record DISPY number of central atom y differencesin cells of the two connected atoms Values correspond to equivalent numbers in CONECT list Possible valuesare 1 0 and 1 18 DISPZ DISPZ 1X 12I6 Zcelldisolacement record DISPZ numberof central atom z differences in cells of the two connected atoms Values cor respond to equivalent numbers in CONECT list Possible val uesare 1 0 and 1 19 END END End of file marker END CAMBRIDGE read only Cerius provides read only support for Cambridge Crystallo graphic Database FDAT format files default file extension fdat Cerius reads only atom coordinates element types crystal cell parameters symmetry operators and bonding connectivity from FDAT files For more information about the FDAT format contact the Cam bridge Crystallographic Database CIF read only Cerius provides read only support for Crystallographic Informa tion File CIF format files Beginning with version 3 0 Cerius could read CIF files generated by the Cambridge Structural Data base to their specification Beginning with version 3 7 Cerius includes a reader that supports more generic CIF files i e files Cerius Modeling Environment April1999 421 D File Formats specified to the minimum requirement for submission to the
374. or entire models from one model space to another see Moving models between model spaces Examining and changing bond lengths Important Changing a bond length manually Cleaning a structure Refining the conformation automatically optimizes all bond lengths You can change bond lengths before cleaning if you want to bias the final structure However if you want a different specific bond length than that determined automatically change it after using the clean function do not use cleaning clean only selected atoms Control of the model cleaning function or change the default properties used for setting bond lengths Bond properties To change the length of a bond manually select the Stretch tool in the Sketcher control panel Then click two bonded atoms The length of the bond in ang stroms is displayed next to it in the model window when you click in empty space To change the length click and drag the cur sor in empty space in the model window Dragging up and or to the right lengthens the bond dragging down and or to the left Cerius Modeling Environment April1999 171 5 Building Models Precise change in bond length Additional information Default bond lengths shortens it You cannot make bonds very unreasonably short or long You can also modify bond lengths by moving selected atoms man ually Translating atoms manually You can also examine bond lengths and other distances with the Measureme
375. or to NO LABEL Cerius Modeling Environment April 1999 243 8 Viewing and Displaying Models Tip Labeling bond attributes Example Additional information Related information y Agila Select the View Display Attributes menu item to access the Display Attributes control panel Set the Label popup under All Selected Atom Attributes to the desired property You can interactively query the current properties of an atom by shift clicking the atom with the right mouse button A message box appears that lists the coordinates and properties of the atom Bonds can be labelled with their fractional bond orders To add or remove labels on all or selected bonds you can Select the View Display Attributes menu item to access the Display Attributes control panel Set the Label popup under All Selected Bond Attributes to the desired property A tutorial example of labeling a model is found in Labeling a model Please see the on screen help for details on the functioning of each control in the Display Attributes control panel and in the toolbar Measuring distances angles planes torsions and inversions for the atoms in a model and displaying these measurements in the model window is discussed under Measuring models Default annotation Basic information that is usually shown by default comprises the model name and model space number in the lower left corner of the model window and a small set of a
376. orial 14 Labeling a model Find the label popup on the toolbar The label popup is this one are ea Fg Set the label popup to ELEMENTS That is click the label popup drag down the list that appears and Cerius Modeling Environment April1999 23 2 Introducing Cerius choose ELEMENTS You can try using the label popup to replace the elements labels with labels that reflect other atomic properties However you have not defined some values such as FFTYPE and CHARGES and these labels display as question marks or zeros You can turn off labeling by setting the label popup to NO LABEL 15 Moving a model You can rotate and translate your model in 3D space You can do this by controlling the cursor with your mouse With the cursor near the middle of the model window hold down the right mouse button and move the cursor vertically and then horizontally The model is rotated around the x and y axes respectively Keyboard shortcut If you have an extended keyboard you can rotate about the x and y axes in large increments by using the left right up and down arrow keys while the cursor is in the model window Now place the cursor close to an edge of the model window and move it parallel to that edge The model is rotated around the z axis Hold down the middle mouse button and move the cursor around in the model window The model is translated i
377. ormation You should already know Tip A color map is a definition of how a quantitative continuous numerical property maps to a specified color range or how a qual itative binary on off property maps to a set of two colors Customized color maps are useful for tasks such as Coloring atoms according to their size or mass Highlighting the backbone atoms of a polymeric model Coloring atoms according to their isotropic temperature fac tors This section includes information on Creating and editing a binary property color map Creating and editing a continuous property color map Editing a property color map Labeling atoms according to various properties is discussed under Labels Color mapping makes use of color ranges so you should have some familiarity with them Color ranges In addition you may want to define custom color ranges to use in your maps Creating and editing a new color range You can display a color range at any time to help in applying it to a map by checking the Show Range check box in the Edit Color Mappings or the Show Color Range check box in any of the control panels in which this control appears 274 Cerius Modeling Environment April 1999 Customizing display colors Creating and editing a binary property colormap Accessing the tools Naming your color map What type of property is to be mapped Setting the on and off colors More colors Select t
378. ose N from the Sketch with popup In the rest of this step you will try to make your model look something like this In the model window click the carbon at the top end of the double bond on the right side of the model You will hear a beep to confirm that you succeeded in hitting the atom Move the cursor up and towards the right A dashed line follows the cursor connecting it with the atom you 12 Cerius Modeling Environment April 1999 If you make a mistake Building a model caffeine clicked and indicating where the bond to your next atom will lie Click in three places to the right of that double bond then click the carbon atom at the bottom end of that double bond forming a 5 membered ring that s fused with the 6 membered ring The new lines are blue ish indicating that all three atoms that you just added are nitrogens The two carbons on the right side of the 6 membered rings now have too many bonds emanating from them And the 5 membered ring might be oddly shaped But don t worry you ll correct these problems later The Sketcher control panel contains an UNDO button It is active only when the previous Sketcher activity can be reversed If you really make a mess of your model you can select the Edit Select All menu item and then the Edit Delete menu item to erase the entire model Then start again at the beginning of Step 5 6 Adding R groups to the basic
379. ou from accidentally overwriting exist ing structure files You may choose and enter an existing filename if you want to overwrite an existing structure file A tutorial example of saving one model is given on Saving a model You can save files in a non Cerius format Some formats allow a choice of formatting options To set them click the Preferences pushbutton to accesses the Save Preferences control panel The controls displayed in this panel depend on what the Save format popup in the Save Model control panel is set to If you want to save only part of a model select the desired part Selecting atoms and groups of atoms cut or copy it and paste it into anew model space Moving parts of models from one model space to another and save the new model Please see the on screen help for details on the functioning of each control in the Save Model control panel and the Save Preferences control panel Model data that can be saved to file include atom coordinates Car tesian fractional or internal element type charge bonding con nectivity crystal unit cell crystal symmetry occupancy and temperature factors The exact combinations depend on the format 210 Cerius Modeling Environment April 1999 File formats Working with C erius sessions you select from the Save Format popup in the Save Model control panel The default MSI file format holds all model data Cerius has its own model file format msi forma
380. ou sketch with predefined molec ular fragments called templates for common structures this is often more convenient than sketching atom by atom 1 Create a model from the phenyl template Click the Template icon on the Sketcher this looks like a co T and is located about halfway down the box icon The current template is phenyl Click in the model window A phenyl ring appears 2 Add a methyl fragment from a template to make toluene Click the Templates button in the Sketcher Double click the organic directory and find the template file methyl Double click methyl A file browser opens on a directory called templates and the template name in the Sketcher changes from phenol to methyl indicating that the methyl template has been successfully loaded Pick one of the phenyl hydrogens The hydrogen atom is replaced by a methyl group to make toluene 74 Cerius Modeling Environment April 1999 Using the 3D Sketcher 3 Add another methyl group Select another of the phenyl hydrogens choose the one farthest away from the methyl group to make p xylene 4 Save the model Save the p xylene structure into a file called xylene msi If necessary see Step 6 on page 68 for a reminder of how to save 5 If you are going to continue immediately with another tutorial Re initialize the program by selecting File
381. own the mouse button and drag the cursor into the current empty display area In other words Click and drag from a noncurrent to a current model space The copied model now exists as two separate models in two separate model spaces To avoid confusion you should rename the current model space so that the name reflects the model that s currently occupying that space or the name of the analog or complex that you intend to construct from the newly copied model For example click the name of the current model in the model table and change it to caffeine analog You can also copy a model into a currently occupied model space if say you want to join them together into a complex or new model Click in an empty part of one of the other display areas and drag the cursor into the current occupied display area The models will be on top of one another but you can move them apart as follows Go to the right atom selection popup on the toolbar of the Visual izer main panel Click and drag to change it from Atom to Frag 40 Cerius Modeling Environment April 1999 Printing a model Click an atom in one of the fragments in the current model space Holding down lt Ctrl gt and the middle mouse button drag that fragment away from the other Make sure both atom selection pop ups are set to Atom when you are finished 34 Cleaning up the display or interrupting this tutorial optional Close the
382. oxes to scale a graph Open the Graph Scaling control panel by choosing the Graph gt Scaling item on the Graphs card or by choosing the Graph Scaling button at the foot of the Graph Man ager Enter a value of 1e5 in the Min X text box and a value of 20 in the Min Y text box Notice the effect on the graph axes Try the zoom and scroll buttons and observe their effect increases the zoom level decreases the zoom level e resets the graph to its original scale You can use the text box associated with the zoom buttons to specify the magnitude of the zoom buttons effect Alter its value from 5 to 20 and notice the effect on the zoom rate 104 Cerius Modeling Environment April 1999 Managing and Modifying Graphs Use the zoom buttons to adjust the graph scale so that the origin of the graph is not visible Now use the scroll buttons until you can see the origin back on the graph The scroll buttons work very similarly to the zoom ones The arrows indicate the scroll directions and the central button resets the scale The scroll text box is used to set the percentage of the axis scrolled in one button click Next you try the mouse keyboard shortcuts for scrolling and zooming Manipulate the graphs with the mouse Try mouse scrolling put the cursor within the axes of the graph and move the mouse while holding down the middle mouse button B
383. p for details on the functioning of each control in the Graph Manager control panel You may need to scale the graph Changing graph axes and scale for the data set s to appear in it Loading graphs Accessing the tools Finding and loading graph files Graphs that have been created and saved to a file Saving graphs can be loaded into a subsequent Cerius session to compare results or to print the graphs Once a graph file has been loaded each graph and its data sets can be manipulated in exactly the same way as those newly created by Cerius see for example Displaying and editing graphs Old and new graphs can be displayed side by side in the Cerius2 Graphs window or old and new data sets can be displayed together in a single graph However Insight and Cerius data cannot be mixed in one graph To load graphs saved from Cerius select the File Load Graphs menu item from the GRAPHS card to access the Load Graphs con trol panel To load graphs saved from Insight II select the File Import Insight TBL menu item from the GRAPHS card to access the Import TBL File control panel Using the file browser in the control panel to navigate the directory structure is fairly intuitive The procedure is described under Load ing model structure files If the name of the file you want to load does not end in grf Cerius or tbl Insight change the name in the filename text entry box as desired see File formats
384. p for details on the functioning of each control in the Playback Script control panel Starting Cerius with a command script file Ordinarily the cerius2 script Starting Cerius2 starts a regular Cerius session that takes its input by means of your interaction with the graphical interface 380 Cerius Modeling Environment April 1999 Ways of automating Cerius Uses of start up command scripts Starting Cerius with an automatic script Controlling Cerius from scripts Cerius can also be run from a recorded script either with or with out the graphical interface You can manually specify the script when you start Cerius or have Cerius always process a certain script automatically without your needing to specify it You can run Cerius from a command script in several ways With the graphical interface automatically process the com mands immediately when Cerius starts then await your addi tional input see Starting Cerius2 with an automatic script and Starting Cerius2 with a specified script With the graphical interface process the commands when you request it then await your additional input see Playing back scripts and log files Without the graphical interface as a foreground job process the commands automatically then exit see Running Cerius2 without the graphical interface Without the graphical interface as a background job process the commands automatically then exit
385. playing annotations data sets the axis lines and numbers or lines indicating cells data set boundaries in 2D graphs that contain periodically repeated data Selecting graphs Selecting and displaying graphs and data sets Selecting which data sets to display and edit for editing are discussed above Specifying immediate or delayed updates of the graph dis play is presented under Selecting graphs to display To change the text of data set keys select the Data Plotting Attributes menu item from the GRAPHS card to access the Plot ting Attributes control panel Alternatively click the Plotting Attributes pushbutton in the Graph Manager control panel to access the Plotting Attributes control panel The controls that are included in this control panel depend on what type of graph is being edited To perform any other function listed under Labeling and annotating graphs select the Graph Annotation menu item from the GRAPHS card to access the Graph Annotation control panel Alternatively click the Graph Annotation pushbutton in the Graph Manager control panel to access the Graph Annotation con trol card To change the text of the x or y axis label enter the text in the x Axis Label or y Axis Label entry boxes in the Graph Annotation control panel To change the text of the graph s title enter the text in the Graph Title entry boxes in the Graph Annotation control panel Several entry boxes are available so you can use
386. ple Enter 0 001 in the Tolerance entry box UNIX command dialog and file samples are represented in a typewriter font For example the following illustrates a line in a grf file CERIUS Grapher File Words in italics represent variables For example gt cerius2 b outputfile scriptfile In this example the actual name of the file to which text output should be directed replaces the value outputfile and scriptfile is replaced with the name of a file containing the desired com mand script 4 Cerius Modeling Environment April 1999 Inttoducing C erius Why read this section If you ve never used Cerius before please go through this section first The idea is just to get you familiar with using basic controls in the interface then you can find details on how to use these and other controls for your own scientific problems in other sections If it s been a while since you ve used Cerius or you just want a quick summary of some basic activities you may start with Start ing Cerius2 and then skip to parts you find interesting This section includes instructions for Starting Cerius2 Building a model caffeine Saving a model What you can do with a model display Building another model ferrocene Reading in additional models Managing multiple models Printing a model Controlling the 3D display Exploring Cerius2 on your own Prerequisites You need to have Cerius already installed on your system
387. pping select the View Graphics Z Clip ping menu item to access the Z Clipping control panel You can perform z clipping in two ways To position the front and back clipping planes independently assure that the Fixed Thickness Clipping check box is unchecked and enter the positions of the back and front planes in the Back and Front Z Clip Plane entry boxes by directly typ ing the values or by using the associated sliders The control panel does not allow you to enter unreasonable values Assure that the Apply Z Clipping check box is checked To specify a clipping slab slice of fixed thickness check the Fixed Thickness Clipping check box and enter the thickness in angstroms in the Z Clip Range entry box by directly typing the value or by using the associated slider Assure that the Apply Z Clipping check box is checked You can adjust the position of the slice along the z axis by using the Back or Front Z Clip Plane controls Please see the on screen help for details on the functioning of each control in the Z Clipping control panel 256 Cerius Modeling Environment April 1999 Model display style Apparent depth effects Depth cueing Accessing the tools Adjusting the perceived depth Additional information Projection Accessing the tools Depth cueing gives models an appearance of depth by displaying objects that are apparently closer to the surface of the computer screen in true color and mixing the co
388. presented on Assigning data types To enter a mathematical expression into the current cell or a selected column you can type the expression in the cell edit win dow illustrated under Accessing the tools and then press lt Enter gt or lt Tab gt or click some other cell to enter the expression Alternatively you can use the Table Properties control panel The Table Properties control panel allows you to in addition enter mathematical expressions into the entire table selected columns or the columns in a named Specifying headings and banners group To access the Table Properties control panel Click the PROPS tool in the table manager tool bar or Select the Data Properties menu item from the TABLES card In the Table Properties control panel set the Properties popup to Derivation to access the Derivation controls then enter your mathematical expression in the Enter Cell Derivation entry box The exact procedure including the character s with which your mathematical expressions begin differ depending on what tool you are using and whether you are applying the expression to the current cell or one or more selected columns To enter an expression in the current cell using the cell edit win dow in the table window start your expression with an equals sign The rest of the expression is made up of one or more of the operators described under Entering mathematical expres Cerius Modeling Environment Ap
389. properties see Property color mapping To color selected atoms according to a cascading series of property color maps click the Multiple Mappings pushbutton in the Color Selected Objects control panel to access the Multiple Color Mappings control panel Use the arrows in this control panel to move selected maps between the Available Mappings and Selected Mappings lists and to change the priority of map application within the Selected Mappings list Then click the APPLY pushbutton Any atoms that are not colored by the first map in the list because they do not have the relevant property or because as is coloring is specified for the relevant map value Creating and editing a binary property color map are colored according to the second map in the list and so on in sequence down the list To return selected atoms to their default element colors click the Reset selected object colors to default action button in the Color Selected Objects control panel You also can set the Pen popup to DEFAULT or click this popup if it is already set to DEFAULT Cerius Modeling Environment April 1999 267 9 Enhancing Model Display Example Additional information A tutorial example of using the Color Selected Objects control panel to color atoms according to a property is found in Coloring atoms according to a property Please see the on screen help for details on the functioning of each control in the Color Selected Objects co
390. r resonant bonds Figure 4 Figure 4 Representation of partial double bonds in 6 membered rings Left Kekule representation of benzene right resonant bonds representation In addition all bonds can be displayed as single lines regardless of the bond order and without changing the actual bond order This is useful for example for simplifying the display when viewing large models at small magnification It does not change the actual bond type which is stored with the model Specifying partial double To set the representation of partial double bonds to resonant bond style dashed lines or Kekule alternating single and double bonds you can Select the Build Edit Bonds menu item to access the Edit Connectivity and Bonding control panel Set the bond order 250 Cerius Modeling Environment April 1999 Specifying multiple bond style Bonds as cylinders Understanding the display Specifying cylinder style Setting the radius Model display style representation popup to RESONANT or KEKULE Click the Convert representation action button or Select the Build 3D Sketcher menu item to access the Sketcher control panel Use the Edit Bond tool Changing the bond type to change the appropriate bonds from single or dou ble to resonant or vice versa To display all bonds in all models as single lines regardless of actual bond type select the View Display Attributes menu item to access the Display A
391. rated in Introducing Cerius2 and described in The Cerius2 Interface Use of the file selection list box and other file selector controls to navigate the directory structure is presented in detail under Find ing model file s A Cerius session consists of all the models and data with which you are currently working as well as application preferences that you have specified Starting a new session Reinitializing Cerius To start a new session select the File New Session menu item Clicking Confirm in the message window that appears reinitial izes Cerius which is equivalent to quitting and restarting Cerius Important All unsaved models and data are lost when you start a new session and settings in control panels are returned to their defaults Saving the current session Making custom directories You can save the current Cerius session at any time After you do so you can then resume that session at some later time as described under Loading a previously saved session either later while you are still running Cerius or after exiting and restarting Cerius You may want to create your own directory or subdirectory in which to save your session To do so go to a UNIX shell window not the one from which you are currently running Cerius cd to the desired parent directory and create your subdirectory with the UNIX mkdir command This can be done at any time For example gt cd CeriusRuns
392. re files Saving individual models is described in Saving model structure files Loading a previously saved session What resuming a session does Resuming a session 2 You can resume a previously saved Cerius session at any time When you load a saved session the current session is reinitialized i e unsaved models and data are lost and settings return to their defaults all models referenced by the resumed session file are loaded into model spaces and application preferences are set to the values indicated in the resumed session file Select the File Load Session menu item from the main control panel s menu bar to access the Load Session control panel This control panel is used to load the session you want to resume Cerius Modeling Environment April 1999 213 6 Managing Modelsand Sessions Use the file selector controls in the Load Session control panel to move through the directory system to find the session you want to resume Either double click the name of the desired session file or select the desired session file and click the LOAD button You can also enter its name in the session name text entry box Important What next Related information Any unsaved models and data in your current session are lost when you resume a saved session and settings in control panels are returned to the values if any set in the resumed session file or to their defaults You can now resume work fro
393. real numbers or as real num numbers bers in scientific notation For either real number format you can enter the number of deci mal places to display in the Decimal Places entry box Changing the display for Cell contents can be displayed in Boolean format as either Yes No mat for Booleans or True False alternatives A value of zero or an expression that evaluates to False is displayed as No or False any other value is displayed as Yes or True and empty cells remain empty Mapping numbers to cat You can display numerical data as a limited set of text items called egories categories Real numbers are rounded to the nearest integer for this purpose Values that round to 1 not zero are assigned the first item in the set For example you might want to display the values 1 2 3 etc as the color names red orange yellow etc To do this you select Cat egory from the list box in the Table Properties control panel and then enter red orange yellow green blue violet in the Categories entry box Numbers that round to 1 2 3 4 5 or 6 are displayed as 330 Cerius Modeling Environment April 1999 Changing the display of text Changing the display for mat of model data Additional information Table style and display red orange yellow etc respectively Numbers outside this range are displayed as lt Unknown gt You can change the display of text from native i e the text as entered to all uppercase or all
394. rectories and load selected files In the Sketcher Template control panel double click organic This opens the directory named organic and displays a list of the file names that are inside that directory Now scroll down the items in the list of filenames by clicking below the slider on the scroll bar to the right of the list box Stop when you see the filename methyl That is click here You can also move the slider by clicking it then dragging it down till you see the methyl filename Click methyl and then click the LOAD pushbutton Cerius Modeling Environment April1999 15 2 Introducing C erius The text next to the template tool in the Sketcher control panel becomes methyl and the template tool is now active highlighted In the model window click the hydrogen atom that s attached to the carbon atom in the upper left part of the 6 membered ring Next click the uppermost N in the 5 membered ring Your model should now look approximately like this 7 Correcting the atom types In the Sketcher control panel find and click the Edit Element tool The Edit Element tool looks like 16 Cerius Modeling Environment April 1999 Building a model caffeine The text entry box for this tool is already set to C Click the middle N in the chain of N s in the 5 membered ring The two half bonds connected to this atom become grey indicat
395. red in Advanced building and editing Displaying labels and other information about atoms in a model is presented in Labels You need to know how to select atoms in your model Selecting atoms and groups of atoms so you can edit them You also of course need to know how to build a model Basic building and or load a model from a file Loading model structure files You may want to review the basics of how the controls in the Sketcher control panel work see How it works This entire section refers to using the Sketcher control panel The 3D Sketcher unless otherwise indicated Most of its editing functions work with both nonperiodic and periodic Other builders systems Changing atoms and their bonding types This section includes Changing the element type Changing the formal charge Changing the bond type Changing the hybridization and adjusting the valence Changing the element type Cerius Modeling Environment April 1999 165 5 Building Models Specifying the element type Tip Changing the element type To change the element type of an existing atom in the model win dow you use the Edit Element tool The edit element type i e the element that you want the atom to become is listed in an entry box to the right of the Edit Element tool Edit Element e E You can change the edit element type in any of several ways Click this entry box and enter an element name in it Choose an ele
396. reen help for details on the functioning of each control in the Disorder control panel After the substitution is per formed information on the number of atoms replaced etc is shown in the text window Intoducing positional disorder Uses of positional disorder Positional disorder is a convenient way to move a model away How it works from a local energy minimum For example you can apply posi tional disorder before cleaning a model see Refining the conforma tion or before performing an energy minimization see the documentation for the Minimizer module in Cerius Simulation Tools Positional disorder randomizes atomic positions atoms are moved by the specified displacement in a random direction Posi tional disorder can be applied to any model type However if an atom in a periodic structure is in a special symmetry position it is not moved from that position although it can be displaced in allowed directions For example if an atom lies on a symmetry Cerius Modeling Environment April 1999 185 5 Building Models Performing positional dis order Additional information axis or plane it and all its symmetry copies is moved only along that axis or within the plane respectively The distance the atom is moved is the component of the random displacement vector that lies on the symmetry axis or in the symmetry plane To introduce positional disorder into a model select the Build Disorder menu item to
397. ries each containing a different cerius2 ini file If Cerius does not find a cerius2 ini file in the directory in which you start it it looks for a cerius2 ini file in your home directory After the initialization file s command script terminates Cerius enters interactive mode awaiting your input To run Cerius from a command script with the graphical interface and have it immediately process a specified command script start Cerius by entering at the system prompt gt cerius2 scriptfile where scriptfile is the name of your command script file Any text output is sent as usual to the text window To run Cerius from a command script with the graphical inter face have it immediately process a specified command script and have it send any text output to a file instead of to the text window start Cerius by entering at the system prompt gt cerius2 o outputfile scriptfile where outputfile is the name of the file that you want to send any text output to and scriptfile is the name of your command script file In either case graphics are displayed in normal fashion in the model window After the command script terminates Cerius enters interactive mode awaiting your input To run Cerius without the graphical interface in background mode enter at the system prompt gt cerius2 b outputfile scriptfile where outputfile is the name of the file that you want to send any text output to and scriptfile is the
398. ril 1999 335 11 Working with Tables sions Press lt Enter gt or lt Tab gt or click some other cell to enter the expression To enter an expression in every cell of a column using the cell edit window in the table window select the column or any cell in it and start your expression with two equals signs The rest of the expression is made up of one or more of the operators described under Entering mathematical expressions Press lt Enter gt or lt Tab gt or click some other cell to enter the expres sion Toenter an expression in every cell of selected column s or the current cell using the Table Properties control panel assure that the Selection control is selected and simply enter your expres sion in the Enter Column Derivation entry box using one or more of the operators described under Entering mathematical expressions Do not begin the expression with an equals sign Click the APPLY TO pushbutton To enter an expression in every cell of the current table use the Table Properties control panel and select the Entire Table con trol Enter your expression in the Enter Column Derivation entry box using one or more of the operators described under Entering mathematical expressions Do not begin the expression with an equals sign Click the APPLY TO pushbutton To enter an expression in every cell of a named group Grouping table information use the Table Properties control panel select the Group control and
399. rius Installation and Administration Guide Select the Utilities Application Licensing menu item in the main Visualizer control panel to access the License Management control panel For all of the functions below select the name of the desired mod ule in the Available Licenses list box This list box shows the names of modules that require licenses and for which you have purchased licenses Cerius Modeling Environment April 1999 383 13 Scripts and Licensing What licenses are avail able Who are using other licenses Reserving licenses Releasing licenses Additional information The Available Licenses list box shows the names of modules that require licenses and for which you have purchased licenses The total number of supported floating licenses i e module spe cific licenses that your site has purchased for a selected module appears near the bottom of the License Management control panel The total number of people currently using floating licenses for that module is listed in the line below the total number supported The login name s of the people using floating licenses for the selected module are shown in the Checked out to list box For token licenses this user list appears only if you currently have the selected feature checked out via token licensing This list of users includes the total number of tokens each person has checked out in parentheses after their name However it does not indicat
400. rius Modeling Environment April1999 97 3 Tutorials 2 Arrange the graphs in the Gallery Open the Gallery Manager control panel by choosing Gal lery gt Manager from the Graphs card In the Graph Chooser list box you will see the names of the three graphs that you ve loaded into the system They are Sorption Loading Plot v1 Emix Fit v1 and Thermodynamics v1 Only the Sorption Loading Plot is on display Click on the Display check boxes next to Emix Fit v1 and Thermodynamics v1 Three graphs should now be on display in the graph window 98 Cerius Modeling Environment April 1999 Managing and Modifying Graphs Huitzogen m 4 o Fat ot taxing ergy 3 3 25 Conon m 20 154 1 HO RNHYo w os Hoo ek g HOt wB hawon 0 i a RON a0 ee 2b 400 eod Pressure Fa x10 Temperature K SORPTION Loading Plet vi Enix Fit vi Freeman Enthalpy Themmodmamics Keal mole Tds B T C T todel 0 2 4 3 8 yol Fraction Molecule 2 Themodmamics v1 Notice that the Gallery Width and the Gallery Height popups on the Gallery Manager control panel are both set to Auto This automatically arranges the graphs to best effect in the graph window Change the Gallery Width to 3 and the Gallery Height to 1 and note the result Try some other width height combina tions before returning both settings to Auto Cerius Modeling Environment April1999 99
401. rol panel 24 Cleaning up the display or interrupting this tutorial optional Close the open control panels if you have too many cluttering up your screen Cerius Modeling Environment April1999 31 2 Introducing C erius Use the File New Session menu item to set all controls to their defaults and remove the model from the model window Reload your caffeine model Or if you want to stop for a while please see Step 13 for exiting Cerius and restarting this tutorial Building another model fenocene If you ve interrupted your tutorial please see Step 13 before start ing this section 25 Adding a new model space You already have a caffeine model but we want to make an additional separate model ferrocene To do this we first make a space to con tain the new model To open an additional model space click the tool just above the model table which is the bottom left part of the Visualizer main panel A new empty model space becomes current and the caffeine model is hidden 26 Sketching an iron atom Ferrocene can be built much faster than caffeine Use the Build 3D Sketcher menu item to open the Sketcher control panel Tron isn t listed in the Sketch with popup you can get it by using the 32 Cerius Modeling Environment April 1999 Building another model fenocene periodic table Click the periodic table tool that s to the right of the Sket
402. ronment April 1999 Finding information Customizing display colors This section includes information on Drawing colors Color ranges Property color mapping Drawing colors Accessing the tools Examining the currently defined colors Changing the standard colors Returning to the preset default colors Cerius enables you to customize the drawing colors pen col ors used in the model window and the graphs window see Working with Graphs You do so by adjusting the relative red green and blue RGB color values of one or more of the 16 stan dard pen colors Select the Utilities Customize Pen Colors menu item on the main Visualizer control panel to access the Pen Colors control panel To display a window showing all currently defined standard col ors click the Show Current Pens action button A Cerius2 Graphs window appears showing all 16 pen colors Alternatively you can show the pen colors as a color range within the model window by checking the Show Color Range check box in any control panel in which it appears e g Property color map ping and selecting PEN_COLORS as the range to display The appropriate color changes when you redefine a color next paragraph To change one of the predefined colors choose its name from the Pen popup in the Pen Colors control panel and use the red green and blue sliders or the entry boxes below them to set the propor tions of red green and blue in
403. ronment April1999 27 2 Introducing C erius 20 Accessing on screen help To obtain help about any control in the Cerius interface Move the cursor to a control about which you want informa tion and click the right mouse button A help panel appears in the center of your screen Right click any other control to replace the help with help about that control Right click a blank area of a control panel to obtain general information about the entire control panel Click left or right mouse button the help window to make the help window disappear or click left mouse button any control panel to make the help window disappear Caution If you click a control while the help window is open that control does perform its usual function 21 Changing the display style Find the display style popup on the toolbar The display style popup is this one 28 Cerius Modeling Environment April 1999 What you can do with a model display Set the display style popup to BALL Try setting the display style to BALL amp STICK and CYLINDER ELLIPSOID POLYHEDRA and TRACE are irrelevant to your current caffeine model You can display different parts of the model in different styles by selecting atom s before applying a style 22 Changing atom colors Select the Build Element Defaults menu item The Edit Elements control panel appears Enter C in
404. rs as highlights on spherical or cylindrical objects Matte surfaces are simulated by a high proportion of diffuse scattering shiny surfaces by a high proportion of specular reflections Diffuse light takes on and in essence defines the perceived color of the object specular light is usually the same color as the light as it leaves the light source A directional light is located infinitely far away from the scene consequently its light rays are parallel A positional light is located at some exact position within the scene A positional light radiates light in all directions from the source unless it is defined as a spotlight A spotlight is a positional light whose light output is restricted to a cone The cutoff determines the width of the cone and the falloff determines its concentration that is the light intensity across a plane that intersects the cone at right angles to its axis Figure 5 Latitude and longitude are defined as for the earth Values towards the north and east are positive those towards the south and west are negative The radius is defined from the center of the viewing sphere Real light is attenuated meaning that its intensity decreases as the distance from the light source increases Light attenuation is 280 Cerius Modeling Environment April 1999 Lighting control Figure 5 Cutoff and falloff in spotlights Looking down from above a plane containing the spotligh
405. rs but not the intermediate values click the More Colors pushbutton to access the Range Mapping Color Selection control panel In addition to controls that are also in the Color Scheme section of the Edit Color Mappings control panel the Range Mapping Color Selection con trol panel allows you to Set the intermediate values i e those that are not outliers toa constant color with the Use Pen or Use RGB Color controls Not apply any color to the intermediate values Use As is con trol Use the Outlier buttons to access Outlier Handling control pan els that govern how values beyond the minimum and maximum values are displayed You can handle outliers in any of several ways Set outliers to a constant color with the Pin to Use Pen or Use RGB Color controls Set outliers to a constant color chosen from the same or a differ ent color range Use Color Range and Use entry number con trols Continue the color range beyond the maximum or minimum values Wraparound control the color range continues beyond the outlier in head to head order i e the order of the colors is not reversed Do not apply any color to outliers Use As is control You can save a custom color map by saving the current Cerius ses sion see Saving the current session A tutorial example of using the Edit Color Mappings control panel to create a color map of atomic mass is found in Coloring atoms according to a property
406. rs designed for constructing more specialized models are available as separate modules and are accessed with the deck of cards menu They have separate documentation Basic building Selecting atoms and groups of atoms Basic editing Advanced building and editing Other builders Cerius Modeling Environment April1999 145 5 Building Models Table 1 Finding information about building models If you want to know about Strategy for building models Example procedure Mouse buttons and keyboard use Adding functional groups Specifying bond lengths angles and torsions Specifying editing drawing etc hydrogen bonds Inverting a chiral center Moving modelsand parts of models Optimizing the conformation Introducing disorder into a structure Adding labels anows etc Changing colorand display style Specifying temperature factors Read Strategy Building a model caffeine Building another model ferrocene Mouse and Keyboard Actions Adding templates groups of atoms Examining and changing bond lengths Hydrogen bonas Inverting about an atomic center Translating and rotating atoms Aligning and positioning atoms Managing Models and Sessions Refining the conformation Introducing substitutional disorder Introducing positional disorder Labeling and annotating models Model display style Enhancing Model Display Temperature factors Changing default propertiesand func
407. s Troubleshooting E If typing cerius2 does not start the program consult the Cerius Installation and Administration Guide for help on setting up the correct environment for running Cerius Select File Load Model to open the Load Model control panel Remember to use the left mouse button for choosing menu items z MSI Model Space O URBEN NEW Frefererces Load the model 135benz msi from the directory Cerius2 Models organics double click the Cerius2 Models direc tory name in the browser box to open that directory dou ble click the organics directory to open the organics directory then double click the 135benz msi filename to load the file Note You may need to use the scroll bar at the side of the file list to locate the organics directory Your model window should look similar to this Cerius Modeling Environment April1999 51 3 Tutorials 1 135berz Troubleshootin 9 If you need to return to the Cerius2 Models directory choose the Run directory selector om at the top right of the browser box aay If you can t find the file in the organics directory make sure that the File Format popup reads MSI and that the text box at the foot of the panel reads msi 52 Cerius Modeling Environment April 1999 Basic GUI Functions 2 Change the display style of the model Use the Display Style popup menu on the left end of the tool bar
408. s press lt F5 gt To adjust the separation drag the mouse in the model window while holding down lt Shift gt and lt Alt gt and the right mouse but ton Use of the left mouse button for selection is disabled during full screen stereo viewing You may find that the stereo option works better for you if you view the model in perspective projection Projection Please see the on screen help for details on the functioning of each control in the Stereo control panel Mouse functions and keyboard shortcuts are summarized in Mouse and Keyboard Actions 290 Cerius Modeling Environment April 1999 oN Working with Graphs Graphical output is generated by a wide variety of Cerius appli cation modules This information is automatically formatted and displayed as a graph The controls in the Graphs module allow you to save and reload graphs and also give you great freedom to manipulate the appearance of the graphs For example you can scale and annotate graphs as well as change the color ranges used to highlight important areas for presentation This section explains This section contains information on Creating graphs Displaying and editing graphs Managing graphs Table 10 Finding information about graphs If you want to know about Finding the Graphs module Types of graphs Displaying orhiding individual graphs Generating series of graphs Plotting valuesfrom a table Starting to edit graphs Editi
409. s 154 building periodic models 191 building specialized models 191 buttons help 131 mouse 131 on control panels 140 C caffeine 8 Cambridge file format 421 card decks 133 adding cards 391 colors 394 creating 390 customizing 390 deleting 391 editing 391 order of cards 391 removing cards 391 renaming 391 saving configuration 391 cards menu 13 436 Cerius Modeling Environment April 1999 cascade panels tool 141 categories defined 330 cations 253 Cerius2 automated 381 background mode 382 controlling with command scripts 379 demonstration of basic activities 5 difficulty starting 7 exiting 47 foreground mode 382 383 interface color coding 395 interface colors customizing 394 introduction 5 names of parts 45 processes 385 386 quitting 47 quitting and resuming a session 22 starting 7 128 starting from desktop 396 startup options 380 who is using 384 without graphical interface 382 383 without startup banner 396 Cerius2 Graphs window 297 Cerius2 Ray Tracing window 288 cerius2 script 128 charge calculating 351 formal 167 181 saving 210 specifying 154 CHARGES 243 check definition 132 chiral center inverting 174 CHIRALITY 243 choose definition 12 132 CLEAN button 178 Cleaner Controls control panel 190 191 cleaning up a conformation 19 changing defaults 190 mode of operation 190 clear panels tool 22 141 393 clear tool 39 click and drag definition 40 131 click definition 10 131 clipboard 20
410. s Stereo menu item to access the Stereo control panel Two stereo viewing methods are available each producing dual images of the current model or models if in overlay mode see Controlling model visibility and the display mode in a slightly differ ent orientation To use the Crystaleyes stereo hardware and glasses from Ste reoGraphics Corporation marketed by Silicon Graphics Inc as Stereo View set the STEREO CONTROLS to CRYSTALEYES and select STEREO To use an ordinary stereo viewer or view in stereo by crossing your eyes set the STEREO CONTROLS to STEREO PAIR and select STEREO For viewing with a stereo viewer set the popup to DISTAL Cerius Modeling Environment April 1999 289 9 Enhancing Model Display Keyboard shortcuts Note Related information Additional information For viewing cross eyed set the popup to DISTAL or PROXI MAL whichever works for you In distal mode the left eye image is on the left side of the screen and the right eye image on the right in proximal mode the images are reversed Adjust the Stereo Separation control to optimize your comfort and ease in interpreting the model The separation affects the apparent flatness or three dimensionality of the model To return to mono display select MONO on the Stereo control panel or press lt F4 gt on the keyboard To toggle between mono and stereo display press lt F4 gt To toggle between Crystaleyes and stereo pair mode
411. s and or columns set the Find Within option to Selection To search within groups if any are defined in the current table Grouping table information set the Find Within option to Group and choose the desired group from the Group pulldown To find any string of alphanumeric characters enter what you want to look for in the Find entry box The associated popup must be set to Text To search for exact matches to your entered characters assure that the Where Cells Are popup is set to an equals sign To search for values that are greater than or less than etc your entered char acters see What constitutes a find Cerius Modeling Environment April 1999 357 11 Working with Tables Potential text matches are compared with your entered characters as text strings Case is ignored in character matches unless you check the Case Sensitive check box Potential numeric matches are compared with your entered characters as numbers unless you check the Compare Numbers as Text check box To search for all empty cells set the Find popup to Null Cells What constitutes a find To perform tests other than exact matches between the potential matches and your entered characters change the Where Cells Are popup from an equals sign to some other criterion Table 24 Text comparisons are done alphabetically For example searching for cells containing values greater than m would match toluene and xylene but not acetate Tabl
412. s control panel Select the desired grd or mbk file from the list box and click the LOAD pushbutton You can use the browser popup to access directories other than the current one Once you have loaded a file and if the default settings in the Slices control panel are satisfactory click the Create New Slice action button on the Slices control panel to create and display a selected slice for your model You may want to edit the slice now e g by changing the transparency value and redisplaying 372 Cerius Modeling Environment April 1999 Positioning the slice plane Other controls Plot the plane s values Additional information Analyzing 3D grid properties The Edit Slice list box shows the slice s that are currently dis played You can select one by clicking its name in the list box Make sure that none of them is selected if you want to create and display a new slice in addition to those already displayed Check or uncheck the Show Slice check box to indicate whether to display the selected slice Click the Delete Slice action button to delete the selected slice from the display and the list You can change the transparency in the Transparency entry box near the bottom of the Slices control panel A slice is defined by its position and direction The default position and direction are chosen so that the slice passes through the best fit plane to the whole model or any selected atoms A slice is cre ated with a def
413. s during building Bonds can be drawn and then optimized automatically Refining the conformation Alternatively unbonded atoms can be placed in the model window see Precise positioning of atoms during building and then bonds can be calculated for all or selected atoms In either event the calculated bond lengths are based on distance and other criteria For cleaning Cerius uses these criteria in deciding what is the optimum bond length For placing bonds Cerius uses them to decide which atom pairs to join by bonds Elementary bond editing with the Sketcher and the Edit Connec tivity and Bonding control panels is presented under Changing atoms and their bonding types and Editing the structure These tasks include deleting bonds changing the bond type and order and making bonds between selected atoms For more advanced bond editing tasks or for performing several elementary tasks simultaneously select the Build Edit Bonds menu item to access the Edit Connectivity and Bonding control panel You can bond selected atoms or delete bonds calculate bonding from a connectivity map change the bond order and change how resonant bonds are displayed Please see the on screen help for details on the functioning of each control in the Edit Connectivity and Bonding control panel Cerius Modeling Environment April 1999 181 5 Building Models Specifying how bonds are To define the criteria by which bonds are calculated click
414. s marked with red Click the diamond for the different models in the list After trying the other models select phenol to be displayed The model displayed in the window changes with each selection Phenol should be the last one displayed It is possible to display multiple models on the screen at any one time in a variety of display styles The Model Display Selector boxes to the right of the model names under the heading Visible show which mod els are displayed Displayed models are indicated by a filled blue box the visibility indicator The current model is always marked visible Check the Model Display Selector box for xylene The model window divides into border mode and the xylene model Cerius Modeling Environment April1999 79 3 Tutorials appears in the top right corner of the window Select two more models The four models are displayed in border mode with the current model phenol as a large model surrounded by smaller images of the other models 1 1 phenol 80 Cerius Modeling Environment April 1999 Managing Modelsand More 2 Try rotating and translating the models Use the mouse to rotate and translate the models in various Overlay ways ia Mode Grid Mode Notice how all are rotated together rH Border To the left of the Cerius logo are three icons that control display style Mode Click on the middle Display Mode icon to get a gri
415. s red You may want to change these colors for instance if you change the background color of the model display window Background color in model window Select the Build Element Defaults menu item from the main Visualizer control panel to access the Edit Elements control panel If desired access the Periodic Table window by clicking the peri odic table tool in the upper right of this control panel Enter the desired element in the Current Element entry box either by typing it in or by choosing it from the Periodic Table window Choose the desired color from the Display Color popup in the Edit Elements control panel This is now the new default color for that element for the remainder of your current Cerius session or until you change it again A tutorial example of using the Edit Elements control panel to change default element colors is found under Changing atom colors Please see the on screen help for details on the functioning of each control in the Edit Elements control panel Coloring selected objects Predefined pen colors You can specifically color selected atoms and other objects such as annotations see Custom annotations by one of several coloring methods To color selected atom s or other object s with a predefined color you can Select the View Colors menu item to access the Color Selected Objects control panel then choose a color from the Pen Cerius Modeling Environment April 1999 2
416. s the Graphs Expert Functions control panel To retain current graph format settings in future graphs in the cur rent Cerius session after the first graph is output from an appli cation module format it as desired see Displaying and editing graphs For example display only the interesting data points by scrolling along the x and or y axes Scrolling a graph and or by expanding or contracting one or both axes Expanding or shrinking an axis then make sure that the Axis Scaling popup in the Graph Scaling control panel is set to FIXED In the Graphs Expert Functions control panel check the desired Keep Same check boxes to apply features of the current graph s format to future graphs Gallery Content To regenerate only graphs having the same name s as currently displayed graphs Graph Axes To retain the same axis scale Expanding or shrinking an axis and labels Changing text annotations Graph Content To display only data sets having the same name s and to maintain the same plotting order Plot Attributes To use the same style and color Changing line style and color in x y graphs y axis offset Shifting a data set along 306 Cerius Modeling Environment April 1999 Additional information Managing graphs the y axis and key Changing text annotations for data sets hav ing the same names as in the previous graph When a new graph is generated by your application module it is di
417. sas eee eens 93 Before youbegin 6 ee eee 93 Cerius Graphs terminology 0 0000 94 Summary of tutorial 1 6 95 Step by step tutorial kee 96 A Loading graphs and using the Gallery Manager96 a neta a ner lorngannout 10 C Scaling graphs 1 0 cc eee eee 103 D Annotating graphs 0 0 0 0c eee eee 106 E Saving graph files 0 2 0 0 cece eae 107 F Creating new graphs and using expert functions109 Checklist review 0 0 ccc ee eee 116 Related material 0 0 0 0 0c ccc eee eee 117 Basic Molecular Simulation Minimization amp Dynamics 117 A Build a model of the glucose molecule 118 B Minimize the glucose energy 118 C Add water to the system 00 121 D Simulating the behavior of the glucose water system 122 Wihatito donexts radem bud Ree et a a ae ae Be 124 4 The Cerius Interface 127 Starting C Britis e Get tdi Ae Dial Athans 128 Initial layout of the Cerius screen 0000 eee 128 Main control panel 6 6 cece 129 Model window 000 cee cee eee eee 130 Text Wind OW iire beeen s x ane ens cae ee 2 130 vi Ceru Modeling Environment April 1999 Using the mouse the basics n asns eee eee eee 131 Mouse buttons 0 ee eee 131 Mouse activities 0 eee eee 131 Using the main control panel 06 000 e ee 132 em nu bar siii se a eterna ca aaia cath wee 134 The toolbar si sce we ey BAG eae ee peta ee
418. se Coloring atoms by properties Property color mapping I Manipulating lighting and colors see Changing atom colors Controlling the 3D display see also Enhancing Model Display LI Printing a model see Printing a model see also Printing models and graphs LI Accessing on screen help see Accessing on screen help Using the Help menu see also On screen help 48 Cerius Modeling Environment April 1999 Tutonals This chapter contains several tutorials covering the basics of work ing within the Cerius modeling environment The tutorials in this chapter are Basic GUI Functions Using the 3D Sketcher Managing Models and More Managing and Modifying Graphs Basic Molecular Simulation Minimization amp Dynamics Basic GUI Functions This section contains an introductory Cerius Visualizer tutorial It shows you the basics of the GUI including loading viewing and display of simple models manipulating control panels and exiting the program You learn about functions on the menu bar and the tool bar This chapter is divided into three parts Before you begin provides some introductory and back ground information Step by step tutorial gives you specific instructions to follow Review summarizes the exercise by giving a checklist of the skills you ve learned and points you to MSI documentation that provides more detailed information about the functions intro duced in the tutorial exer
419. search is complete the results are defined as a named group To use an existing group as the basis for starting to define a new group you can duplicate the original group To make a copy of an existing group access the Table Groups con trol panel as under Creating a named group from a selection Select the Group tool and enter the name of the group to be duplicated in the Group entry box by choosing its name from the associated popup 354 Cerius Modeling Environment April 1999 Additional information Grouping table information Enter a name for the new group the copy in the Group Name entry box then click the CREATE pushbutton Please see the on screen help for details on the functioning of each control in the Table Groups and Find Cells control panels Editing a group definition Adding rows or columns to a named group Merging existing groups Removing rows or col umns from a group You can add more rows and or columns to an existing named group merge two groups and remove rows and or columns from an existing group To add selected rows and or columns to an existing group access the Table Groups control panel as under Creating a named group from a selection Select the name of that group by clicking its name in the Groups In Table list box Assure that the Selection tool is selected and click the MERGE pushbutton To merge two or more existing groups into a new larger group access the Table Groups contr
420. selecting and deselecting atoms Cerius Modeling Environment April1999 55 3 Tutorials 1 Select an atom Use the left mouse button to pick one of the atoms in the model In stick display when the atom is selected it is highlighted Cerius beeps to let you know that you ve selected the atom The atom is also identified in the text window Select several more atoms by holding down the lt Shift gt key as you select them You should now have three or four atoms highlighted in the model win dow Change the display style Use the Display Style popup to change to Ball amp Stick Note that the new display style only applies to the selected atoms In the ball and the cylinder display styles selected atoms are indicated with thin stripes 3 Select and deselect all atoms Deselect all atoms by clicking on empty space in the model window 56 Cerius Modeling Environment April 1999 Basic GUI Functions a 3 Find the Select All and Deselect All a il icons on the tool bar They look like the icons in the margin Next you use these buttons to select and deselect atoms in the model window Choose the Select All button then changethe Display Style popup to Ball All the atoms in the window are highlighted and then appear as balls wrapped in thin blue lines Choose the Deselect All button All the atoms are deselected t
421. ses sion you may find it useful to save the list of active control panels to a file that is read at startup time for subsequent sessions To cause certain oT panels to be automatically opened when ever you start Cerius open the desired control panel s if they are not in the Active Control Panels list in the Panel Manager control panel select their name s in that list click the Toggle startup flag action button so that an asterisk appears next to each desired name in the list and then click the SAVE CONFIGURATION pushbut ton see How it works for additional information To specify that a control panel no longer be displayed automati cally upon startup select its name in the Active Control Panels list click the Toggle startup flag action button so that the asterisk next to its name disappears and click the SAVE CONFIGURA TION pushbutton To save the current list of active control panels along with the specifications as to which ones are and are not displayed automat ically upon startup see Automatic panel display click the SAVE CONFIGURATION pushbutton in the Panel Manager control panel When you click the SAVE CONFIGURATION pushbutton the list of active and automatically displayed control panels is saved Cerius Modeling Environment April 1999 393 14 Customizing the Interface Additional information to a file named panels in an MSIguirc subdirectory in your home directory This file is automatically read wh
422. set annotation color and line width see Editing the annotation objects For filled circles the fill color is the same as the outline color To add text to the model display you use the Text tool Specify the text content by entering it in the entry box to the right of the Text tool Then select the Text tool and click the left mouse button in the model window to place the text annotation The new text annotation object uses the currently set text content annotation color font style and size see Editing the annotation objects You can use the annotation tools discussed in this section in two ways To specify the defaults for new annotation objects set the desired controls before placing the annotation object in the model window To change the properties of existing annotation objects use the selection tool to select one or more annotation objects and then set the desired controls 246 Cerius Modeling Environment April 1999 Moving resizing and removing annotations Labeling and annotating models To set or change the color of any annotation object use the color popup to the right of the Line tool in the control panel Addi tional color controls can be accessed by clicking the More Colors pushbutton This brings up the Color Selected Objects control panel see Model display colors To specify that rectangles or circles be drawn in filled or outline style check or uncheck the Filled check box The fill
423. shbutton to access the On Color Selection or Off Color Selection control panels respec tively In addition to controls that are also available in the Edit Color Mappings control panel these control panels allow you to Define a custom color by using the red green and blue sliders or the entry boxes below them to set the proportions of red green and blue in the color Cerius Modeling Environment April 1999 275 9 Enhancing Model Display Saving a color map Additional information Select any color entry number from any already defined color range You can save a custom color map by saving the current Cerius ses sion see Saving the current session Please see the on screen help for details on the functioning of each control in the control panels mentioned in this section Creating and editing a continuous property color map Accessing the tools Naming your color map What type of property is to be mapped Setting the range of prop erty values Select the Utilities Customize Color Mappings menu item from the main Visualizer control panel to access the Edit Color Mappings control panel Alternatively if you have the Color Selected Objects control panel open Accessing the tools you can click its Edit Mappings pushbutton to access the Edit Color Mappings control panel Type a name in the New Map entry box Enter it by pressing lt Enter gt on the keyboard or clicking elsewhere in the control
424. sibility of polymer back To display only the backbone atoms of a polymer select the View bones Atom Visibility menu item to access the Atom Visibility control a carbon trace of proteins panel Click the Hide Non Backbone Atoms action button You must have previously defined some atoms as backbone atoms using the Polymer Builder tools You can also use this control panel to hide hydrogen atoms or any selected atoms or to display all or selected atoms To display an alpha carbon trace of a protein model Set the display style popup on the toolbar to TRACE or Cerius Modeling Environment April 1999 255 8 Viewing and Displaying Models Additional information Select the View Display Attributes menu item to access the Display Attributes control panel Set the Style popup to TRACE Please see the on screen help for details on the functioning of each control in the Atom Visibility and Display Attributes control pan els Cross sections of models Accessing the tools Additional information You can control the apparent location of the viewing plane along a line perpendicular to the computer screen as well as the plane s thickness so as to view either the whole model or a cross section slice or slab through it You do this by clipping the view between two coordinates of the screen z axis that is to set the apparent dis tance of the viewing plane from the computer screen To control and apply z cli
425. single and double buffergraph ics mode Decrease magnification of model view zoom out Increase magnification of model view zoom in Reset model view Fill window Rotate model up by 45 Rotate model left by 45 Rotate model down by 45 Rotate model right by 45 Table 37 Moving cursor in table window with keyboard Use keys on an extended keyboard noton a numeric keypad Keys lt Exc gt lt Tab gt Action Canceland undo editing Enter value if any and move to the cell to the right of the current cell Entering your changes lt Tab gt lt Shift gt Activate the cell edit window Editing cell contents lt Enter gt Enter value if any and move to the cell below the curent cell Cerius Modeling Environment April 1999 413 C Mouse and Keyboard Actions Table 37 Moving cursor in table window with keyboard Use keys on an extended keyboard noton a numeric keypad Keys Action lt S gt Move to the cell above the curent cell lt gt Move to the cell to the left of the current cell in cell edit window move one character to the left lt l gt Move to the cell below the curent cell lt gt Move to the cell to the right of the current cell in cell edit window move one character to the right any other Activate the cell edit window and start entering characters 414 Cerius Modeling Environment April 1999 MsSl format structure files Other format structure files Te
426. sion for any reason you may do so now without losing any of your work To quit simply select the File Exit menu item and then click Exit in the Exit option window that appears To resume this introduction to Cerius cd to the directory that you made in Step 1 and start Cerius as in Step 2 To reload your caffeine model select the File Load Model menu item In the Load Model control panel s file browser double click left mouse button the name of the file that you saved in Step 11 which should be caffeine msi 22 Cerius Modeling Environment April 1999 What you can do with a model display Close the Load Model control panel if you don t want it cluttering up your screen What you can do with a model display If you ve interrupted your tutorial please see Step 13 before start ing this section Now that you have a model what kinds of things can you do with it in the Visualizer module of Cerius The Visualizer module is the one you ve been using It includes the controls that are accessed from the Visualizer main panel s menu bar and toolbar as well as those on the left side of the Visualizer main panel The stack of cards on the right side of the Visualizer main panel gives access to other modules Note This section shows you various ways of modifying the display of a model None of its activities are required if you re mainly interested in features introduced in later sections of this tut
427. sions to cells or col umns The os componentsand main control panelof The Cerius2 Interface Cerius 404 Cerius Modeling Environment April 1999 Glossary Cerius Modeling Environment April 1999 405 B Definitions 406 Cerius Modeling Environment April 1999 This section includes Additional information Mouse and Keyboard Actions This section summarizes mouse and keyboard actions organized according to what part of the Cerius interface the cursor is over To find mouse and keyboard actions organized according to what tasks you want to perform please see the relevant sections of this documentation This section summarizes Mouse actions Keyboard shortcuts A graphical table of mouse actions in the model window can be accessed by selecting the Help Topics Mouse Operations menu item in the main control panel to access the Model Window Mouse Operations control panel A table of keyboard shortcuts that apply to the model window can be accessed by selecting the Help Topics Keyboard Operations menu item in the main control panel to access the Model Window Keyboard Operations control panel Mouse actions This section summarizes what mouse button and simultaneously pressed key on the keyboard if any to press and what mouse action to take in order to perform various activities when the cur sor is Over Control panels Graph window Model window Cerius Modeling Environment April 1999 40
428. splayed in the same format It can be reformatted if necessary as described under Displaying and editing graphs Please see the on screen help for details on the functioning of each control in the Graphs Expert Functions control panel Preventing replacement of old graphs Controlling graph replacement when many graphs are generated and when graphs are loaded from files Accessing the tools Some Cerius modules can produce a series of similar graphs overwriting the previous graph with the new one In addition when you load a graph from file it usually replaces those dis played in the graph window For example a graph of energy vs minimization step can be pro duced by the Minimizer module each time a minimization is run and in the Rietveld module each refinement produces a new dif fraction data set The graph and data set s from the preceding run are lost when this happens The default is to overwrite any old version of these graphs with the newest one This prevents many versions of obsolete graphs from accumulating in the graph window and in computer memory How ever if you want to retain old versions of graphs along with the new ones you can Place the new graph in the graph window next to the old graph or Place the new data set in the same graph along with the old data set As another example when a graph file is loaded the graphs in the file usually replace those currently shown in the grap
429. sponds to the position of the color in the range Creating and editing a new color range Accessing the tools Naming the color range Defining the color range Tip Select the Utilities Customize Color Ranges menu item from the main Visualizer control panel to access the Edit Color Ranges control panel Alternatively if you have the Color Selected Objects control panel open Accessing the tools you can click its Color Ranges pushbutton to access the Color by Range control panel and then click the Edit Ranges pushbutton to access the Edit Color Ranges control panel Type a name in the New entry box Enter it by pressing lt Enter gt on the keyboard or clicking elsewhere in the control panel Default values appear for the number of colors in the range and the num bers of the critical entries Choose the number of color entries from the Number of colors in range pulldown More numbers give you smoother color grada tions but you shouldn t set the number so high that it s beyond of your computer s graphics capability Set the colors of the critical entries at either end of the range by using the red green and blue sliders or the entry boxes below them to set the proportions of red green and blue in the color You can display your new color range at any time see Viewing color ranges to help in defining it The display is updated as you change the definition of the color range Add an additional critica
430. ssing the CLEAN button does not make it exactly symmetrical If you have purchased one of the QUANTUM 1 applications ADF DMol3 GAUSSIAN MOPAC or Zindo you may use their sym metry function to fully symmetrize the model Click the popup above the deck of cards it should be labeled BUILDERS 1 on the right side of the Visualizer main panel and choose QUANTUM 1 The menu card for any of these quantum chemistry applications contains a Geometry Symmetry menu item Select it to access a Symmetry control panel Change the Tol 34 Cerius Modeling Environment April 1999 Reading in additional models erance popup to COARSE Click the Find symmetry action but ton Reading in additional models 28 Reading in more models Click the File Load Model menu item to access the Load Model control panel In the control panel double click Cerius2 Models and then double click one of the subdirectory names If you obtain another list of subdirectories double click the desired one Double click the name of any model you think might be inter esting A third model space is created displaying the chosen model Both the caffeine and ferrocene named Model2 model spaces are hidden Locate the model table in the lower left of the Visualizer main panel In the list of model names click Model2 and type fer rocene then press lt Enter gt You may save the ferrocene model if you want Use the Load Model
431. supplied by MSI File formats Handling multiple models You can change how files of a particular format are interpreted as they are read in For example whether to use any periodic infor mation contained in the file whether the number of hydrogen atoms is to be checked and corrected whether and how to fill in possible missing bonds etc To access these additional controls click the Preferences button in the Load Model control panel which gives access to the Load Preferences control panel The controls displayed in this panel depend on what the File Format popup in the Load Model control panel is set to Please see the on screen help for details on the functioning of each control in the Load Model control panel and the Load Preferences control panel Cerius supplies databases for a wide range of types of molecules and materials These databases are contained in subdirectories of the Cerius2 Models directory accessible from your run directory during Cerius sessions These subdirectories include models of catalysts ceramics metals minerals molecular crystals mono mers organics polymers sorbates and others Many file formats besides the MSI format see File Formats can be imported if you need to use model files obtained from other pro grams or databases However transfer of all model data cannot be guaranteed when reading files that are not in MSI format Handling multiple models Why read this section Fin
432. t Aset of radii angles and value coordinates for a 2D polar plot 94 Cerius Modeling Environment April 1999 Graph Gallery Gallery Graphs Data Sets Managing and Modifying Graphs At the middle level of the hierarchy is the graph A graph is made up of one or more data sets displayed on axes At the top of the hierarchy is the gallery The gallery is the name given to the group of graphs on display in the graph window at a given time X Y Graph 2D Polar Coordinates 2D Contour Plot Cerius Modeling Environment April1999 95 3 Tutorials Summary of tutorial The tutorial is divided into six exercises A Loading graphs and using the Gallery Manager B Using the Graph Manager and setting plotting attributes C Scaling graphs D Annotating graphs E Saving graph files F Creating new graphs and using expert functions Step by step tutorial This section takes you through a series of short progressive exercises designed to familiarize you with the Cerius Graphs card A Loading graphs and using the Gallery Manager Graphs are saved in files with grf extensions this format is described in the File Formats appendix of the Cerius Modeling Environment Files generated using Insight II can also be loaded these have the extension tbl and are described at the MSI website www msi com The sample graphs that you load for this tutorial were created by the Blends module and the Sorpti
433. t capable of stor ing every detail of any model in the Cerius modeling environ ment You should always store your model files using the msi format unless you want to exchange them with databases other molecular modeling applications or your own programs Many file formats besides the msi format see File Formats can be written if you need to transfer model files to other programs or databases However transfer of all model data cannot be guaran teed when writing files that are not in msi format Saving all models To conveniently save all models in the current session save the session rather than its individual models Saving the current ses sion Working with Cerius sessions Why read this section Finding information This section tells you what Cerius sessions are and how to start resume and save them It is useful if you for example want to Resume a session that you had to interrupt earlier Save all your models at once Return Cerius to its start up state Always start your sessions with Cerius in a certain state This section includes information on Starting a new session Saving the current session Loading a previously saved session Using saved sessions as preferences settings Cerius Modeling Environment April1999 211 6 Managing Modelsand Sessions You should already know What is a session The basics of starting Cerius and using its interface are demon st
434. t degrees Constants In addition to numbers that you type in you can use any of the physical constants shown in Table 17 Table 17 Physical constants in Cerius table expressions Constant e h k n pi r Description Base of the natural logarithm 2 71828 Planck s constant 9 53709 E 14 kcal sec mol Boltzmann s constant 3 2998 E 27 kcal mol deg Avogadro s number 6 02204 E423 particles mor Pi 3 14159 Gasconstant 1 98717 E 3 kcal mol deg SMARTS table derivations The following derivations can be entered as column headers in the QSAR study table 342 Cerius Modeling Environment April 1999 Cross references To columns rows Valuesand mathematical expressions daysss Structure and daysss_unique Structure For example daysss Structure clcccccl daysss_unique Structure C H1 NOH In writing expressions you can refer to columns rows groups or cells in the current table and to columns rows groups or cells in other tables These references are evaluated as numbers text or models depending on the content of the items that are referred to Examples of expressions including cross references are sqrt col 4 sqrt column 4 sqrt col Concentration sqrt Concentration sqrt col H2S04 Conc mean row 6 mean row TG sum group query results 5 You can refer to a column in any expression The syntax for column cross refer
435. t and the center of its light beam The spotlight islocated at the origin and the beam points directly upwards The cufoff is the half angle of the cone of light in degrees Line c shows the light intensity vs distance from the beam scenter with a higher falloff value than used forline b Line a showszero falloff i e the inten sity is the same across the beam of light simulated by multiplying the intensity of light from a given source by an attenuation factor attenuation factor k kd 1 d q where d distance between the light and the object k a con stant k the linear attenuation factor and kg the quadratic attenuation factor Attenuation applies only to positional lights since they are located at a defined distance from the scene Additional information The book by Neider et al 1993 contains a good discussion of lighting that can help in understanding and using the Cerius lighting controls Cerus Modeling Environment April1999 281 9 Enhancing Model Display Accessing the tools Tip Example Additional information Select the View Graphics Lighting menu item to access the Lighting control panel Unless you also have a solid surface dis played make sure your model is displayed in some style other than stick or trace Atom and bond display styles since lighting has no effect on lines or points It is often helpful turn off all other lights when you are defining alight You ca
436. t cell if no column is selected or the entire table choose the desired data type from the Column Cell Data Type list box Assure that Selec tion Entire Table or Group is set as desired then click the APPLY TO pushbutton Cerius Modeling Environment April 1999 329 11 Working with Tables Additional information Please see the on screen help for details on the functioning of each control in the Table Properties control panel Setting display formats You can assign a display format to selected column s containing numeric Boolean text or model data You can also assign a dis play format to the current cell or the entire table These formats affect only how numbers are displayed the full number is retained in computer memory and stored with the table Accessing the tools To assign or reassign display formats for numeric Boolean or model data access the Table Properties control panel as above see Accessing the tools and set the Properties popup to Format to access the Format controls To assign a display format to the selected column s the current cell if no column is selected or the entire table choose the desired format see below from the list box Assure that Selection Entire Table or Group is set as desired then click the APPLY TO push button Changing the display for You can display numbers as integers real numbers are rounded to mat for integers and real the nearest integer as floating point
437. t the View Reset View menu item in the main control panel Press lt Alt gt r on your keyboard Press lt Home gt on an extended keyboard 236 Cerius Modeling Environment April 1999 Defining the center of rotation Centering the model Additional information Moving models on the screen Select the View Orient menu item to access the Orient View control panel Click the RESET VIEW pushbutton The center of rotation of a model is the centroid of all or selected atoms By default all atoms are used To redefine the center of rota tion for the current model select the desired atom s Selecting no atoms is the same as selecting all atoms Then you can do any of Select the View Set Origin menu item in the main control panel Press lt Alt gt o on your keyboard Select the View Orient menu item to access the Orient View control panel Click the SET ORIGIN pushbutton Centering a model translates it so that its center of rotation is in the center of the screen Centering does not change the viewing angle or magnification Centering immediately after defining the center of rotation see Defining the center of rotation affects only the cur rent model Centering after some other change in the model view moves all models in concert To center the model s you can do any of Select the View Center menu item in the main control panel Press lt Alt gt t on your keyboard Select the View Ori
438. t to be used i e Biso or Uiso for isotropic tem perature factors and Uj Bj or Bj for anisotropic temperature factors see Table 3 Enter the value of the isotropic temperature factor or the values for the anisotropic temperature factors The six anisotropic temperature factors are entered as a matrix Cerius Modeling Environment April 1999 189 5 Building Models Command line Additional information YEL U12 U13 U22 U23 U33 Click the Use Isotropic or Use Anisotropic action button to change the temperature factors of the atom to isotropic or anisotropic using the format and value s specified If you specify the anisotropic temperature factors from the com mand line you should enter them in the order 1 1 2 2 3 3 1 2 2 3 1 3 Please see the on screen help for details on the functioning of each control in the Added Atom Temperature Factors control panel Loading and saving temperature factors As mentioned Conventions and Table 3 several formats exist for describing temperature factors When temperature factors are loaded from or saved in structure files the factors are automati cally converted to and from the Cerius format The MSI SHELX CIF ICSD DBWS and MolEN structure file for mats can all be used to store isotropic and anisotropic temperature factors please see File Formats for more details Isotropic temperature factors but not anisotropic factors are stored in both xtl an
439. t want all data sets in a selected graph to displayed or if you want them to be displayed in different styles you need to select the data set How to select a graph for display and editing is discussed under Selecting and displaying graphs If you already have the Gallery Manager control panel open Accessing the tools click the Graph Manager pushbutton in the Gallery Manager control panel to access the Graph Manager con trol panel Alternatively select the Graph Manager menu item from the GRAPHS card to access the Graph Manager control panel To display or hide particular data sets check or uncheck the appro priate check boxes in the Display column to the left of the list of data set names in the Graph Manager control panel To enable the display style etc of data sets to be edited check or uncheck the appropriate check boxes in the Edit column to the right of the list of data set names in the Graph Manager control panel Please see the on screen help for details on the functioning of each control in the Graph Manager control panel Labeling and annotating graphs You can change labels for graph axes and data set keys and enter text for a graph title You can also specify whether to display the axis labels the title above the graph the color code key to the Cerius Modeling Environment April 1999 299 10 Working with Graphs Related information Accessing the tools Changing text annota tions Dis
440. table tool bar See Copying one or more cells and Moving cutting one or more cells for copying or cutting information into the clipboard The Cerius table clipboard holds the contents of only the one most recent copy or cut operation Pasted rows and columns are always inserted into the table the pasted information does not replace the contents of any selected row s or column s If both rows and columns are selected for the copy or cut opera tion Cerius asks you before pasting whether you want to past the rows or the columns into the current selection The results are more intuitively predictable if only contiguous columns or only contiguous rows are selected during copying or cutting If no region is selected before pasting or if the selected region is differently shaped than the contents of the clipboard the paste operation fills down and to the right starting from the top cell in the selected column the left most cell in the selected row or if no row or column is selected the current cell You can use this feature to copy or move a column or row to a dif ferent part of the target column or row For example you can copy Cerius Modeling Environment April 1999 323 11 Working with Tables Clearing one or more cells Technical notes on cut ting deleting and clear ing rows 1 4 of a column to rows 5 8 of the target column You do this by clicking row 5 of the target column before pasting You can off
441. tarting a new empty graph Specifying the type of graph Selecting data to plot Loading graphs Cerius Modeling Environment April 1999 293 10 Working with Graphs Related information You should already know Controlling which one s of several plots which are held in com puter memory during a Cerius session are displayed in the Cerius2 Graphs window is discussed under Selecting and displaying graphs How to access the Graphs module is described under Accessing the tools Starting a new empty graph Accessing the tools Creating a new graph Additional information Select the Gallery Manager menu item from the GRAPHS card to access the Gallery Manager control panel To create a new graph check a check box in the Display column to the left of the blank line below the last name if any in the list of graph names in the Gallery Manager control panel Check the Edit check box to the right of the name User Graph v of the new graph Make sure all other Edit check boxes are unchecked Please see the on screen help for details on the functioning of each control in the Gallery Manager control panel Specifying the type of graph Concepts When you create a new graph you need to specify whether the graph should be an x y graph a 2D Cartesian graph or a 2D polar graph For automatically created graphs the type of data deter mines what type of graph is used to display it An x y data set is an ord
442. tem s native window manager and also for certain model manipulation activities Right button the help button Used to obtain help text for GUI controls For details see On screen help The actions of the mouse buttons can differ depending on whether the cursor is over control panels in the model window or over tables or graphs A summary of all mouse button functions is contained in Mouse and Keyboard Actions Mouse activities Definitions Certain words are generally used in indicating what to do with the mouse Unless otherwise specified they always mean to use the left mouse button The types of controls are described under Types of controls Click move the mouse so as to place the cursor over the con trol or other item mentioned and then press and immediately release the left mouse button Double click place the cursor over the control or other item mentioned and then click the left mouse button twice in succes sion relatively quickly Click and drag place the cursor over the control or other item mentioned and then press the left mouse button and while keeping the button depressed move the cursor to the item mentioned and then release the button when the cursor is over Cerus Modeling Environment April 1999 131 4 The Cerius Interface that item For menus popups and similar controls a list of items usually appears as soon as you click Select choose set the popup to a value et
443. the Current Element text entry box Change the Display Color popup to some color other than dark grey You can change the default colors for other elements in a similar way 23 Coloring atoms according to a property The functionality covered in this optional step is actually rather advanced but it is new with release 3 0 of Cerius2 so users interested in new features may find it useful Select the View Colors menu item The Color Selected Objects control panel appears If we had defined a property such as charge or moveability we could select all the atoms Cerius Modeling Environment April1999 29 2 Introducing Cerius in the model and then simply click one of the items in the Color by a Property list to color the atoms However we haven t So we will define our own property color map Click the Edit Mappings pushbutton in the Color Selected Objects control panel to access the Edit Color Mappings con trol panel The Edit Color Mappings control panel appears Enter the name Mass in the New Map entry box choose Mass from the Attribute popup and set the Type popup to CON TINUOUS Set the Minimum and Maximum Attribute Values between which the color range is to extend to 0 5 and 15 5 respectively Check the Use Range check box and choose PEN_COLORS from the Use Range popup You can label atoms with their mass if you want The atomic masses range from 1 01 H to 16 00
444. the Pref calculated Additional information Specifying automatic determination of bond types Additional information Calculating bonds erences pushbutton to the right of the Calculate connectivity check box in the Edit Connectivity and Bonding control panel to access the Bond Calculation Preferences control panel Covalent general Slater i e atomic and where appropriate metallic radii are stored for each atom Depending on the selected Bonding Method the appropriate radius is used in bond calcula tions The stored radii can be edited by specifying an element and method and then entering the radius in the corresponding radius entry box These radii can also be changed with the Edit Elements control panel Element properties You can also define a Bonding Tolerance effectively the propor tion of the relevant atomic radius to be used in looking for con tacts For example if the tolerance factor is 1 5 and the ideal bond length is 1 4 A abond is created if the two atoms are within 2 1 A 1 4 x 1 5 of one another You can inhibit the creation of bonds to certain categories of ele ments that is alkali metals transition metals and lanthanides actinides during bonding calculations using the appropriate check boxes This inhibition works by effectively zeroing the bond ing radius for a given atom Inhibition of bonding to a specific ele ment can be achieved by actually zeroing the bonding radius for that elem
445. the TABLES card Using the file browser in the control panel to navigate the directory structure is fairly intuitive The procedure is described under Load ing model structure files Cerius Modeling Environment April 1999 319 11 Working with Tables Interpreting the file con tents Importing the data Additional information The file extension dat is present in the filename entry box by default but you may use any extension Enter the name of the file containing tabular data Since Cerius has no way of automatically knowing how the data is presented in the file you need to specify whether the file con tains row and or column headings labels and what characters are used in the files to indicate new lines within text strings to delimit text strings and to separate columns If you are not sure of the file s format you can examine it with any text editor Alternatively you can load the file with the Import Table control panel Importing the data examine the loaded table in the table window and then if necessary close the table Closing a table without saving any changes and then re import it with dif ferent specifications Double click the name of the desired file or select it and click the IMPORT pushbutton in the Import Table control panel Cerius creates a new table from the imported data adding an untitled entry to the list of tables Please see the on screen help for details on the functioning of each
446. tialization scripts 381 output 382 383 processing when requested 380 recording 376 377 379 repetitive tasks 380 381 running 380 382 startup scripts 381 tables 348 uses 376 381 using 379 Command Tracing control panel 378 379 commands copying log file 377 displaying 379 levels 378 logging 376 377 379 managing log files 377 monitoring 378 replaying 379 restarting log file 377 RUN LOG file 377 ole log file 377 ective logging 377 text window 379 se se tracing 378 computer screen apparent distance from 257 conformation cleaning 19 178 Connect tool 157 connect definition 157 Connolly surface definition 223 Connolly surfaces creating 224 loading 225 saving 225 Connolly Surfaces control panel 224 226 Connolly M L 223 399 contact surfaces 223 control panels active definition 392 and current table 316 automatically opening at startup 393 buttons 140 closing 22 140 393 closing all 136 392 colors 394 illustration of controls 138 managing 22 392 opening 141 392 organizing on screen 136 393 saving active list 393 saving configuration 393 searching 136 control panels definition 138 controls colors 140 dials 176 label with ellipsis 140 labels 140 shape 140 sliders 176 types 140 typical illustration 138 coordinate systems 153 175 176 177 187 interconversion 187 model window 231 saving 210 coordination number 253 correcting hydrogens 19 covalent radius 179 critical entry defin
447. ties and Vector Preferences control panels 226 Cerius Modeling Environment April 1999 Vector properties Cerius Modeling Environment April 1999 227 7 Geometry Analysis 228 Cerius Modeling Environment April 1999 Viewing and Displaying Models The Cerius e Visualizer allows you to position models as desired to move models relative to one another and control how models are displayed and printed You can also annotate them with labels and arrows etc and animate models according to the results of certain calculations This section explains This section tells you how to accomplish Moving models on the screen Animating models Labeling and annotating models Model display style Resolution and graphical quality Printing models and graphs Table 6 Finding information about viewing models If you want to know about Read Mouse buttons and keyboard use Mouse and Keyboard Actions Rotating moving and magnifying the model Moving models on the screen view Moving parts of models Editing the structure Transfering modelsorpartsof modelsbetween Moving models between model spaces model spaces Docking models Moving models relative to one another Superimposing models ms matching Superimposing models Continuous rotation or rocking of models Changing the default mouse rotation action Scaling the view Changing the view magnification Size of the model window Maximum size Cerius Modeling Environm
448. to the target might also be selected depending on your selection criteria Selection can apply to only the single atoms actually picked or to all atoms with the same name same element type or same force field type or to all of a bonded set of atoms a fragment or of the smallest set of bonded atoms leading away from the main model and starting after the selected atom short end To change the default behavior i e picking individual or contig uous atoms change the select what popup on the toolbar see The controls from Atom to Name Element FF forcefield type Frag ment or End short end Names atoms are not present in all mod Cerius Modeling Environment April 1999 161 5 Building Models Selection is within How it works Additional selection crite ria Additional information els but may be defined in other Cerius modules which are documented separately You can also name atoms with the Edit Selected Atoms control panel Atom properties Depending on the setting of the pick target popup you can also select all residues of the same Type or Identifier or all chains of the same Name The default is to select all atoms in a residue chain or model In addition to the selection criteria you can restrict or expand the selection scope for example whether atoms are selected in the cur rent model or all models etc To change the default selection scope i e within the current model use the
449. tool If the hybridization type option is already correct you can activate the Edit Hybrid tool by clicking it You can change atoms in the model window to the hybridization type specified in the hybridization type popup in several ways Select the Edit Hybrid tool and then pick the desired atom s Select the desired atom s Selecting atoms and groups of atoms and then double click the Edit Hybrid tool You can change the hybridization before adding an atom by using the Add Atom control panel Precise positioning of atoms during building You can also edit the hybridization of existing atoms and other properties simultaneously with the Edit Selected Atoms control panel Changing the element type together with other properties Editing the structure This section includes Deleting atoms and bonds Duplicating parts of a model Examining and changing bond lengths Examining and changing angles Cerius Modeling Environment April 1999 169 5 Building Models Examining and changing torsions Inverting about an atomic center Translating and rotating atoms Aligning and positioning atoms Deleting atoms and bonds Deleting atoms and asso To delete an atom and all bonds leading to it use the Delete Atom ciated bonds tool in the Sketcher control panel You can Select the Delete Atom tool and then pick the atom s to delete or Select the desired atom s and then double click the Delete Atom tool to delete
450. tool in the Sketcher control panel or the Edit Delete menu item in the main control panel Deleting atoms and bonds If any of the automatic tools give the wrong number of hydrogens at some atom s you can change their hybridization state Chang ing the hybridization and adjusting the valence formal charge Chang ing the formal charge and or the bond type between that atom and another heavy atom Changing the bond type and then adjust the hydrogens again Selecting atoms and groups of atoms Why read this section You need to select one or more atoms when you want to perform some function e g editing labeling changing the display style on only certain atoms You can select atoms individually or according to some criterion such as acommon property or their membership in a group Selec tion criteria may be quite complex This section contains information on Selecting and deselecting individual atoms 158 Cerius Modeling Environment April 1999 Selecting atomsand groupsof atoms Selecting atoms in several models Selecting and deselecting collections of atoms Customized atom selection The controls The Edit pulldown menu and the toolbar in the Visualizer s main control panel offer several ways of selecting one or more atoms There are also four atom selection tools in the toolbar Selectall tool A Deselectall tool Pick target popup Selec twhat popup Example Several ways of selecti
451. tors Statistical operators Table 14 take one argument This argument must refer to a collection of numeric data such as a column a row or a group consisting of numeric cells Statistical operators return null if anything else is specified Examples of expressions including statistical operators are mean col 1 max row TG sum group query results In general statistical operators should be used only in cell expres sions not column expressions The column row and group referred to Cross references in this example all contain numerical values Table 14 Statistical operators in Cerius table expressions Operator Retums Description avg number Numeric mean mean number Numeric mean same asavg median number Median value sum number Sumofall values min number Minimum value max number Maximum value range number Numeric range abs max min 340 Cerius Modeling Environment April 1999 Values and mathematical expressions Table 14 Statistical operators in Cerius table expressions Operator Retums Description count number Numberof non null values in the data set stdev number Standard deviation of the population n var number Variance of the population n skew number Skewness kurtosis number Kurtosis Statistical transformations Statistical transformations Table 15 take one argument that must refer to a column of numeric values They return null if anything else is specified
452. ttom to top while holding down the left mouse button increases a value e g a bond length and drag ging in the opposite direction decreases the value An UNDO button provided at the top of the control panel can be used to cancel one or a series of previous commands for many types of operations The UNDO button is greyed out when it is not usable Checking the Guide check box gives you on screen help in the upper left corner of the model window on the 3D Sketcher Detailed examples of using the Sketcher control panel to build caf feine Building a model caffeine and ferrocene Building another model ferrocene are included in this guide Other basic building tools Other building tools are also accessed from the Visualizer s Build menu Use of some of these is covered under Advanced building and editing but others have functions that are similar to those in the 3D Sketcher control panel Among the latter are the Add Atom Edit Atoms Edit Bonds and Edit H Bonds menu items Most of these enable better control over exactly how the controls operate than does the 3D Sketcher control panel and may there fore enable faster building under certain circumstances These alternatives to the sketcher often provide full support of periodic models in areas where the Sketcher does not for example to add atoms to a periodic system you have to use the Add Atom control panel rather than the 3D Sketcher control panel
453. ttributes control panel Click the Pref erences pushbutton to access the Style Preferences control panel Uncheck the Highlight Multiple Bonds check box To display the bond types again simply check the Highlight Mul tiple Bonds check box Cylinder style is similar to stick style except that the bonds are represented by cylinders providing a more three dimensional representation Atoms are not specifically shown but are present at the ends of bonds The bond colors represent the element types of the atoms at each end To display bonds in cylinder style you can Set the display style popup on the toolbar to CYLINDER or Select the View Display Attributes menu item to access the Display Attributes control panel Set the Style popup to CYL INDER To set the radius of the cylinders click the Preferences button in the Display Attributes control panel to access the Style Preferences control panel Enter the desired radius in the Cylinder Radius entry box Cerius Modeling Environment April 1999 251 8 Viewing and Displaying Models Lone atoms Understanding the display Specifying lone atom style Atoms as balls Understanding the display Specifying ball style Setting the radii Ball and stick models Understanding the display Lone not bonded atoms in a model can be represented as three dimensional crosses small spheres or simple points or can be not displayed at all To change how lone at
454. tween the fragments The fragments that are rotated are those that result in the fewest atoms being moved or Select the desired atomic centers and then double click the Invert tool to invert the chirality at all selected centers simulta neously Inversions cannot be done for centers that are part of complex ring structures i e for those in which one fragment makes more than two attachments to the selected atomic center You can examine inversions with the Measurements control panel Inversions Translating and rotating atoms Translating atoms manu ally Translating atoms pre cisely You can translate selected atoms in all three dimensions by using the mouse to control the cursor in the model window To translate selected atoms Inthe x y plane Drag the cursor while holding down lt Ctrl gt and the middle mouse button Along the z axis Drag the cursor while holding down lt Ctrl gt lt Alt gt and the middle mouse button If symmetry constraints do not allow the requested translation the closest permitted translation is made instead Tables of mouse button and keyboard combinations are included in Mouse and Keyboard Actions To translate selected atoms a precise distance in a specified direc tion select the Move Atoms Translate menu item to access the Translate Atoms control panel You can specify the direction in Cartesian XYZ crystal ABC or surface UVW coordinates or specify th
455. ubdivisions made to simulate depth cue ing of vectors as well as to the number of subdivisions made to the triangles created during sphere cylinder ellipsoid and surface tessellation To adjust the graphics quality select the View Display Attributes menu item then click the Preferences button in the Display Attributes control panel In the Style Preferences control panel that appears set X PostScript Quality to STANDARD BETTER or EXCELLENT Each higher quality setting can increase both the file size and the rendering time by a factor of four over the next lower quality setting Please see the on screen help for details on the functioning of each control in the Style Preferences control panel Printing models and graphs Why read this section Related information This section includes information on Printing models and graphs as hardcopy You can print full color greyscale or dithered black and white PostScript images Converting model and graph displays to PostScript files PostScript files can be printed later You can transfer them to other applications to edit them They can also be imported into other applications such as desktop publishing packages for use as illustrations Setting the print resolution is discussed in Resolution and graphical quality Using PSYCHO within Cerius for rendering models and producing PostScript output is discussed in Rendering and ray tracing Cerius Model
456. uide line will reappear If you click directly on the existing carbon you won t generate a second atom Click somewhere else to put down a second atom and con tinue to build a ring of six carbon atoms terminate the ring by clicking on the original atom You should now have a hexagonal form somewhat similar to this in the model window You can correct any mistakes with the Undo button 3 Set the sketching mode back to Selection Highlight the Selection mode icon once more so that all future clicks in the Model window do not result in new atoms 4 Adjust the hydrogens and minimize the structure Click the H Adjust button The H Adjust command adds or deletes hydrogens to all atoms in order to satisfy their valences In this case H Adjust adds two hydrogen 66 Cerius Modeling Environment April 1999 Using the 3D Sketcher atoms to each of the carbon atoms Hold down the Clean button Release the button when the atoms stop moving Clean attempts to adjust bond lengths and angles to reasonable values Note that recleaning after manipulating or deforming the structure may find a different structure Clean You have built a cyclohexane ring The cyclohexane ring that you see on the screen is probably in the chair conformation 5 Experiment with the display and view of the model Try altering display styles and rotating and rescaling the model to view it If you
457. users of Cerius and should be of interest to all users regardless of the type of work you are doing or the application modules you are using Enhancing Model Display might also be used by a technical graphic artist in collaboration with a scientist user of Cerius You should already be familiar with The windowing software on your workstation Use of the mouse on your workstation Basic UNIX commands Your workstation should have A licensed copy of Cerius installed A home directory in which you have write permission Additional information sources On screen help On screen help is available within the Cerius environment It is accessed by clicking the right mouse button while the cursor is over the item in the interface about which you want information 2 Cerius Modeling Environment April 1999 Other Cerius documentation A brief identification of some items appears when you simply allow the cursor to linger over them Additional help and some demos are accessed from the Help menu Other Cerius documentation 2 You can find additional information about Cerius in several other documentation sets Cerius Builders Discusses the specialized builder modules that can be added to supplement the basic model sketching capabilities provided by the Cerius modeling environment that is the Analog Builder Crystal Builder Surface Builder Interface Builder Polymer Builder and Amorphous Build
458. uto check box is checked If the Auto check box is unchecked you need to click the SHOW pushbutton to update the graph window Turning off automatic updating can be faster if you are dealing with graphs containing many data points which may therefore be slow to update You can allow Cerius to set the graph window width and height automatically by setting both the Gallery Width and Gallery Height popups to AUTO If you prefer some other width and or height set the Gallery Width and Gallery Height to the desired numbers of columns and rows respectively of graphs to display You can find the coordinates of any point on any type of graph by pressing lt Ctrl gt on the keyboard and left clicking a point in the graph The information is displayed in the text window 298 Cerius Modeling Environment April 1999 Selecting graphs for edit ing Additional information Displaying and editing graphs To enable graphs to be edited check or uncheck the appropriate check boxes in the Edit column to the right of the list of graph names in the Gallery Manager control panel Only graphs of the same type Specifying the type of graph can be edited simultaneously Please see the on screen help for details on the functioning of each control in the Gallery Manager control panel Selecting which data sets to display and edit Related information Accessing the tools Selecting a data set Additional information If you do no
459. utorials Materials Science and Life Science A Build a model of the glucose molecule 1 Construct a glucose model To start Cerius enter cerius2 in a UNIX window After Cerius starts open the 3D Sketcher from the Build pull down and construct a model of glucose See Using the 3D Sketcher for guidance on using the 3D Sketcher Click and hold the CLEAN button in the Sketcher control panel to clean the structure 118 Cerius Modeling Environment April 1999 Basic Molecular Simulation Minimization amp Dynamics B Minimize the glucose energy During a molecular mechanics simulation the movement of the atoms the changing of bond lengths angles etc and the interac tions between non bonded atoms and molecules are controlled by a mathematical function usually referred to as the forcefield The accuracy of a molecular mechanics simulation depends critically on the choice of forcefield The PCFF forcefield has been shown to give accurate models of a wide range of organic molecules and polymers and is used in this tutorial Information about other forcefields and theoretical background about atomistic level simulation using molecular mechanics can be found in the Forcefield based Simulations book 1 Load the forcefield Open the OFF SETUP card deck and locate the OPEN FORCEFIELD card Load the pcff_300_1 01 forcefield You may need to scroll down through a number of other
460. vert text to uppercase Cerius Modeling Environment April 1999 347 11 Working with Tables Binary text operators Binary text operators Table 21 are placed between two values both of which must evaluate to characters Table 21 Binary text operators in Cerius table expressions Operator Retums Description text Concatenate text strings forexample A B produces AB cattonumber number Converta category to its comesponding ordinal format text Format an entity based on a C style format string in the second argu ment e g format col Activity 8 3f numbertocat text Convert an ordinal numberto the conesponding category Categories are described under Mapping numbers to categories Table and command operations Table operators Table operators Table 22 take no arguments They return the row or column number of the current cell Table 22 Table operators in Cerius table expressions Operator Retums Description row number Curent row index col number Curent column index Command operators Command operators Table 23 enable you to run Cerius com mand scripts and or evaluate Tcl Tool Command Language expressions and return the results to table cells These operators take a single argument that must evaluate to one or more Cerius commands or one or more legal Tcl commands For more informa tion about Cerius and Tcl commands refer to Cerius Command Script Guide 348 Cerius Modeling En
461. vironment April 1999 Values and mathematical expressions Table 23 Command operators in Cerius table expressions Operator Retums Description eval any Evaluate a Cerius or Tcl command and return the result soute any Open the file named in the argument evaluate each Ceru or Tcl com mand in that file and retum the result Recalculating table values How it works When you type in or edit an expression for a column or cell using the cell edit window in the table window Cerius calculates and displays the value of the derivation as soon as you enter the deri vation by pressing lt Enter gt Entering mathematical expressions If you use the Derivation pane of the Table Properties control panel Entering mathematical expressions to enter or edit an expression Cerius calculates and displays the value of the derivation as soon as you click the APPLY TO pushbutton If you change the values in a column row group or cell that is referred to in another cell or column s expression the values in that cell or column are not recalculated until you request that the table be recalculated Recalculating table val To recalculate all the expressions in the current table ues H Click the RECALC tool in the table manager tool bar or Select the Data Recalculate menu item from the TABLES card To select a cell column or row and also send to Cerius any com mand that has been associated with that cell column or row by
462. wed by any num ber of Object Definition Blocks ODB followed by a termination record Header record A header must be the first record of the file It is of the form CERIUS Grapher File 428 Cerius Modeling Environment April 1999 Grf Comments Any subsequent line of the file can be a comment line in which the first character must be an exclamation point Such lines are ignored by the file parser Object definition bloc ks X Y data set ODB Initiation record Each ODB is an independent unit although it may be referenced from other ODBs A single ODB may define a single Data set Set of plotting attributes This references one data set ODB Graph This references any number of data set ODBs Gallery This references any number of graph ODBs Any record that begins with a greater than symbol that is gt is considered to mark the beginning of an ODB and the end of any previous ODB Subsequent records of the ODB are single record token descriptors in the form of a token in capital letters followed by a value The only exceptions to this are graph title descriptors and data value descriptors both of which occupy multiple records In the following description terms enclosed in brackets are values strings extracted from the file by Cerius Where such val ues have been expressed in capitals these represent the range of accepted values All token descriptors within an
463. wever the task orientation rather than tool orientation as well as ample use of headings and labels should facilitate your finding information no matter what approach you use This guide does not necessarily replicate control specific information that can be found by using the on screen help A few of many possible approaches include Build a model using carbon atoms and available templates then edit the element and bond types as desired Add hydrogens as the heavy atom skeleton is being built or after it is complete Keep the conformation and topology as correct as possible while building a model or build a distorted model and then adjust its conformation and or connectivity Add several identical templates simultaneously at several points of a base model then edit the individual functional groups as needed Build a small model copy it edit both copies as desired and then join the fragments into one larger fragment Build small fragments then use them as the basis for construct ing larger models or as starting structures for use with the more specialized builders available as other Cerius modules Load templates from disk then edit fuse and or connect them to form a larger fragment Load or generate a periodic system Other builders then edit it 148 Cerius Modeling Environment April 1999 Basic building The 3D Sketcher You access the 3D Sketcher by selecting the Build 3D Sket
464. with Cerius2 sessions Table 4 Finding information about managing models and sessions If you want to know about Controls in the model manager Finding files with file browsersin control panels Mouse buttonsand keyboard use Model databases supplied by MSI Building models Labeling and annotating models Printing models Saving models Saving only part ofa model Saving all models in a Cerius session Model data File formats Making your own directores The current model Read The model manager Loading model structure files Mouse and Keyboard Actions Models supplied by MSI Building Models Labeling and annotating models Printing models and graphs Saving individual models Saving part of a model Saving the current session What is saved as a model File Formats Making custom directories Specifying the current model Cerius Modeling Environment April 1999 195 6 Managing Modelsand Sessions Table 4 Finding information about managing models and sessions If you wantto know about Read Model spaces adding and removing Creating clearing and deleting model spaces Naming models Model visibility Renaming models Controlling model visibility and the display mode Displaying a model in the model win Controlling model visibility and the display mode dow Moving a modelorpartofa model Moving models between model spaces between model spaces Non C erus applications Re
465. with its transformed coordinates Additional information Moving models on the screen display axis or around a user defined center of rotation and axis You can define the center of rotation and rotation axis by entering values in the Rotation Center and Translate Rotate Axis entry boxes or selecting some atoms and then clicking the associated DEFINE pushbuttons in the Model Space Transforms control panel When you save the model in msi format Saving model structure files both its original coordinates and the transform for generating the transformed coordinates are automatically saved Please see the on screen help for details on the functioning of each control in the Model Space Transforms control panel Mouse func tions and keyboard shortcuts are summarized in Mouse and Key board Actions Supenimposing models Accessing the tools Specifying the models Specifying the atoms to superimpose You can superimpose or match models by performing a least squares fit between selected atoms Whole nonperiodic models or the asymmetric unit of periodic models can be superimposed One model is translated and rotated as a rigid unit to obtain the best rms fit of the selected atoms with those of a reference or tar get model This is useful for comparing structures of all or parts of models Select the Move Atoms Match menu item to access the Match Models control panel Specify which model is the reference model
466. xes indicating the viewing angle lower right corner You may hide this information if you prefer In addition you may want to show a scale bar and or a large set of axes in the model window 244 Cerius Modeling Environment April 1999 Accessing the tools Additional information Labeling and annotating models To change the default information shown in the model window select the View Options menu item to access the View Options control panel Check or uncheck the appropriate View Annotation check boxes Please see the on screen help for details on the functioning of each control in the View Options control panel Custom annotations Accessing the annotation tools Annotating your model Select the Build Annotation menu item to access the Annota tion control panel The Annotation control panel contains several types of tools to help you highlight and enhance your displayed model To add lines to the model display you use the Line tool Select the Line tool then click the left mouse button in the model window to place one end of the line Without releasing the mouse button drag the line out by moving the cursor then release the mouse button to place the other end of the line The new line uses the currently set annotation color and line width see Editing the annotation objects To add arrows to the model display you use the Arrow tool Select the Arrow tool then click the left mouse button in t
467. y QUADRANT is for polar systems XMIN ordinate angle in degrees In Cartesian graphs this is the center of the first pixel XMAX ordinate angle in degrees This equals xmin width ordinates per pixel Y IN ordinate In Cartesian graphs this is the center of first pixel YMAX ordinate radius This equals ymin height ordinates per pixel XSIZE width This is the number of data points in each row YSIZE height This is the number of rows of data 430 Cerius Modeling Environment April 1999 Grf DATAPOINTS points This must be the last record of the ODB It is followed by points width height blank delim ited real values X Y plotting attribute ODB Initiation record Descriptors 2D plotting attribute ODB Initiation record Descriptors gt PLOT XY METHOD name version name and version These refer to an X Y data set ODB within the file COLOUR color One of the Cerius colors for example RED PIN YEL etc The default is WHI white STYLE LINE POINT HISTOGRAM DELTA DELTA TIC The default is POINT YOFFSET ordinate The default is 0 0 LABEL string This is the label to appear on the key The default is the string Undefined gt PLOT 2D METHOD name version name and version These refer to a 2D data set ODB within the file STYLE CONTINUOUS CONTOUR DELTA Datarepresentat
468. y and their rays are therefore parallel Concepts Accessing the tools To convert a positional light Positional lights into a spotlight and adjust the spotlight click the Spotlight pushbutton in the Light ing control panel to access the Spotlight Settings control panel Wiath of the spotlight To control the width of the spotlight adjust the Cutoff control A value of 180 means the positional light is not a spotlight and only cutoff values between 0 and 90 have any meaning see Figure 5 Tip It can be helpful to use a very wide beam at first Cutoff set to 90 adjust the spotlight direction Aiming the spotlight and then narrow the beam Otherwise you can narrow the beam so much that none of its light hits the model Aiming the spotlight To illuminate the model a spotlight not only has to be located at the desired position as defined and displayed in the Lightsource Position control panel Positional lights but also needs to be pointed in the correct direction To adjust the direction in which the spotlight shines use the Spot light Direction controls in the Spotlight Settings control panel You would generally want the direction to proceed from the posi tion of the spotlight towards the model You might want to start your adjustments by setting the spotlight s latitude to the negative of its positional latitude and the spotlight s longitude to its positional longitude plus 180 subtract the result i
469. y moving the mouse diagonally you can scroll in both the x and y directions at once Try mouse zooming put the cursor within the axes of the graph and move the mouse while holding down both the lt Shift gt key and the middle mouse button Click the Zoom Reset button to return the graph to its orig inal scale Cerius Modeling Environment April 1999 105 3 Tutorials Click the Axis Scaling popup to view the choice of scale set tings Then click again using the right mouse button to dis play the help text that describes the five sorts of scaling When you have finished reading the help text click it to make it disap pear Try the Auto XY setting and then the Nice XY setting Notice the change in the Max Y value when you do this Exit from the Graph Scaling control panel D Annotating graphs In the following steps you learn how to use the Annotation Option popups to display or not display graph axes and various text items You also edit the text for the graph title and axes Remember you ve already learned how to edit the text for the graph key or legend in the Edit the Label text box step on page 102 1 Experiment with the Graph Annotations Open the Graph Annotation control panel by choosing Graph gt Annotation from the Graphs card or by clicking the Graph Annotation button at the foot of the Graph Manager 106 Cerius Modeling E
470. y table window appears 314 Cerius Modeling Environment April 1999 Current table tool bar Curent cell information window Introduction to Cerius tables Column headings Curent cell Cell Row headings Table manager tool bar Table manager list of tables Sections of the table win dow The two major sections of the table window are the upper main table section which displays the contents of the current table and the lower table manager section which lists all tables currently in computer memory and under the control of the Table Manager window This table manager does not necessarily keep track of tables created by other Cerius applications for example the C eQSAR module s Study Table The tools in the current table tool bar affect only the current table see Specifying the current table and can be used to change parts of the table Examples include specifying alignment grid type and numeric properties formatting and activities like cutting copy ing and pasting values The tools in the table manager tool bar operate on tables as a whole Examples include creating a new table and opening an existing Cerius Modeling Environment April 1999 315 11 Working with Tables table as well as saving and closing a table You do not need to select any portion of the table to perform these types of activities Keeping track of the cunent table How it works Precautions Caution
471. your working direc tory in the Working Directory entry box This directory must already exist If more than one executable can run on the chosen machine select the name of the desired executable in the Executable list box You can also enter the complete path and file name of the executable in the Executable entry box The registry information contained the list boxes in this control panel can become outdated if changes are made after Cerius was installed at your site To update this information your installation administrator needs to edit the applcomm db file For additional information on this file please see the Cerius Installation and Administration Guide You can start the specified Cerius process on an external host in two ways To save the settings for use later in the current session so that the process is started as instructed only when you access the application module from its menu card click the Save Selec tion action button To start the process immediately click the Start action button The process starts but does not do anything other than wait for your additional input from the application module s menu card To stop running the selected Cerius process on the specified host click the Kill action button You would typically use this button if you want to restart the selected process on another host Please see the on screen help for details on the functioning of each control in the Process Mana

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