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Maestro Manuals and Tutorial

1. 105 MENU button 5 reote nint 7 Mol file format converting to from 200 molecular representation ALOMS sciiti 61 bonds 62 default 64 SAVINO allieta 25 Molecular Representation panel Atoms folder ere 62 Bonds folder ee 63 OPO MING is d rnit e etre 61 Ribbons folder 66 Settings folder narici 65 Molecular Surface panel 125 molecular surfaces see surfaces molecules connecting and fusing 40 drawing cialis 36 37 See also structures Monitor panel eee 168 Mopac file format see 19 mouse functions generalista aan 5 Project Table mE Workspace i idea 72 multiple bonds creating in Draw mode 37 multi structure files exporting to mutating residues Maestro 6 5 User Manual Index N New Plot dialog DOX sss 114 O online HEP diiniita 179 opening state of project reverting to 101 P panel layout saving iii 137 panning PlOts cian 116 partial charge assigning in 46 pasting values into the Project Table 97 PDB atom names assigning 46 PDB file format conversion 200 PDB files color scheme used on import 21 PDB residue name
2. 32 COLOFN E astutos 141 displaying for hidden atoms 142 field descriptions in 142 A 68 placement 141 NA A ea iden 69 Update 69 Limit Surface panel n 135 lin plots iran ira 115 local transformations 72 74 Markers for iaa 74 YOA ON Sisia toD dne 74 switching to ciclina 73 translations eee 74 M MacroModel file format converting tOMPOM lana 199 Macros patiel coria 155 macros creating nen 155 Maestro Citing USE Of cocer nein 1 file format se 185 file format example 187 helps 179 main WIDndOW ritieni tiones 6 starting 3 workflow paradigm u 11 Make Dir creating directories with 78 Maestro 6 5 User Manual markers Advanced Transformation 74 displaying een 103 H bond and contact measurement 106 measurement geometric 104 MDL SD file format converting to from 202 measurements angles eterne 103 creating properties from 106 dihedralSs 103 distances ient itia 103 dummy atoms eene 107 H bond and contact 105 writing to a file 106 Measurements panel Contacts folder 105 Distances folder 104 H Bonds folder
3. 108 ihr C 74 rSh command nn 163 S Save Image panel sse 159 Save PlotXY Image panel 122 Save Project As project selector TI Schrodinger contact information 182 Schr dinger web site sss 182 schrodinger hosts file 163 166 SCP COMMANC c ii 163 scratch directory ii 161 162 specifying in hosts file 165 SGEatch entry aor RP 12 scratch files see temporary files scratch projects icones 11 75 scripts see command scripts utility scripts SD MDL file format converting to from 202 SD MDL file extracting structures from 204 searching for text iii 85 Select menu Select panel selecting atoms eene 53 selection state rana 80 SEQUENCE VIEWEL ui ul 7 series see plots SOUS 109 creating with Boolean operators 110 reading and writing 111 selecting atoms for 109 Sets Boolean panel ss 111 Sets Panel iaia 110 Show Property panel 100 Show Hide Commands panel 152 Sitemap panel urico 129 Sitemap surfaces 127 131 smoothing wire bondSs 63 snapshot undoing with eee snapshot of project
4. cnn nrnnonanos 103 9 2 1 Measuring Distances Angles and DihedralS 103 9 2 2 Displaying Hydrogen Bonds and Contacts ne 105 9 2 3 Storing the Results of Measurer ents iicet tenter penne 106 9 2 4 Defining Dummy Atoms for Measurements eee 107 93 SUPSHMIMPOSINS SUHOEDUEGS coiere pere reU ORE ete e ES e PEUT 107 pd c m P E 109 9 4 1 Creating and Deleting Sets rer ether iret 109 942 Selecting Atoms TOF a Set escas terrenae Ani 109 9 4 3 Creating Sets With Boolean Operators eee 110 9 4 4 Reading and Writing SetS i 111 9 5 Assigning and Aligning Protein Structures i 111 Chapter 10 Blotting M 113 10 1 Creating Plots ae 113 10 2 Viewing and Manipulating PIOtS i 114 10 2 1 Selecting Plots eee te retener neve tte pea 115 10 2 2 Panini aud Zo eo eter tet Pe e ettet ht epa 116 10 2 3 Labeling and Unlabeling Data Points eee 116 10 2 4 Selecting and Deselecting Project Entries esses 117 10 2 5 Including and Excluding Project Entries esses 117 10 3 Editing Plots and Plot Sef ngs enndem tte 117 10 3 1 Modifying Plot Attributes 2 essas rrr ertt 118 10 3 2 Operating on Plot Series io etit asia 119 10 3 3 Changing X and Y Axis Display sere 120 10 4 Updating Plots to Reflect Pro
5. 157 159 scratch ENtry iii 12 toolbar iicet eerte 7 10 X XYZ file format eie eiii torte 19 Z zooming O ER n 116 in Workspace esee 71 Maestro 6 5 User Manual 120 West 45th Street 1500 SW First Avenue 3655 Nobel Drive Dynamostrafe 13 32nd Floor Suite 1180 Suite 430 68165 Mannheim New York NY 10036 Portland OR 97201 San Diego CA 92122 Germany SCHRODINGER
6. 138 12 2 3 Setting Project Synchronization and Storage Preferences 139 12 2 4 Specifying a Default Working DIrectory ii 141 12 2 5 Customizing Atom Label Appearance eee 141 12 2 6 Setting Mouse Preferente ni 142 12 2 7 Setting Pile Suffix Preferentes aie dent deett 143 12 2 8 Setting Builder Preferences iii 144 12 3 Customizing te Works pateks veian 145 12 3 1 Showing or Hiding Controls and Displays esses 146 12 3 2 Setting the Background Colof illa 146 12 3 3 Specifying a Stereo Viewing Method sese 146 12 3 4 Enabling Perspective ccein ninina eii ta EEI Ee 147 12 3 5 Enabling Fobia da 147 12 3 6 DEP CUES sionista 149 12 4 Creating Command Aliases eiecit tn Gas erica 150 Maestro 6 5 User Manual vii Contents 12 5 Customization Using Command Scripts conos 151 12 51 Command st oi he 151 125 2 Biuldimns a Command SCIL Eee esee ge aenea nene DIES 152 12 5 3 Saving a Command Sernpt ui re ttis reg eR 153 12 5 4 Opening Existing Command Scripts ess 153 12 5 5 Running and Stopping Scripts eben tte repete 153 12 5 6 Customizations You Can Perform With a Script 153 12 6 Creatina MACIOS occur nidad ORE ere da 155 Chapter 13 Printing and Saving Workspace Images ess 157 13 1 Prinung an Image File or Printer oerte e ede 157
7. ALT U Deselect all entries Select gt None ALT X Exclude selected entries Entry gt Exclude ALT Z Undo Redo last command Edit gt Undo Redo in main window 8 3 5 Configuring the Project Table The Project Table panel provides tools for controlling what is displayed in the table Some of these tools are also discussed later in this chapter Displaying a subset of entries You can display a subset of entries by selecting the entries then choosing Show Only from the Entry menu and likewise you can hide the selected entries by choosing Hide from the Entry menu To redisplay all entries choose Show All from the Entry menu Displaying a subset of properties You can display a subset of properties by choosing Show from the Property menu then using the Show Property dialog box to select the prop erties to show or hide You can choose individual properties or a family of properties Property families are the properties generated by an application such as QikProp Resizing rows and columns You can resize rows or columns by dragging the border of the row or column using the middle mouse button You can also set the width of the columns to the width of the widest data item the width the widest of the data and the heading or to a fixed width by choosing from the Columns button menu on the toolbar or the Columns submenu of the Table menu Swapping Title and Entry name In the non scrolling area of the project table you can display either t
8. Contents Appendix A The Maestro File Format oocooomossosssss 185 Al Basic File Description cer eee Rettore che ricette tx poo cese ariani 185 A 2 Data Block cm ae aa 185 A 3 Compressed Format s ence aaa ae 187 A 4 Data Item Names nnion e dia 187 AS Example Maestro Pile oeann tertie te i E E 187 Appendix B Atom Types svsrrrisririsricirazescioreosivearicaianinionenioninazonis ioni cioninie 191 Appendix C Entry Suffixes cicc cccscssescessssessosscessevnassoossnsesssssnsssosseesssosssossenns 197 Appendix D WG itt tC 199 D I Structure Conversiofi sipres 1 aaa 199 D 1 1 Conversions to and From MacroModel Format 199 D 1 2 Conversions to and From Mol2 Format eese 200 D 1 3 Conversions to and From PDB Format pdbconvert 200 D 1 4 Conversions to and From SD Format sdconvert 202 D 2 Str cture BXISOUIOD iure err o P ERO its 203 D3 Display of Properties assista ps corte teret reti 205 DA Structure PrepatatlOD o c rre rite ttt perta ti 206 A 209 Innoc 211 Maestro 6 5 User Manual ix Contents x Maestro 6 5 User Manual Chapter 1 Document Overview This manual contains an introduction to the Maestro graphical user interface GUI and a description of how to use Maestro s settings panels and fe
9. Once you have displayed the structure specify the part of the structure to be mapped with the tools in the Part Of Structure To Map section You can pick atoms in the Workspace enter an ASL expression click All or click Select to open the Atom Selection dialog box and select atoms If Show Markers is selected a dark pink trace is superimposed on the selected atoms and bonds To clear the atom selection click Clear Clearing the selection does not delete existing sitemaps Sitemap sitemap Six Job sitemaptmp Login dya11 Host localhost 1 Source of job input 4 Workspace lt gt Selected entries Part of structure to map ASL ces AI Select W Pick Entries W Show markers Bounding box ASL miga Select LJ Pick Entries W Show markers Box margin 6 00 Grid spacing Standard Start Write Job Files Hide Help Figure 11 4 The Sitemap panel Maestro 6 5 User Manual 129 Chapter 11 Surfaces 11 2 4 Defining the Mapping Box In addition to specifying the structure for which a sitemap is to be generated you must also set the location and size of the box of atoms to be mapped using the tools in the Bounding Box section You can pick atoms in the Workspace enter an ASL expression click All or click Select to open the Atom Selection dialog box and select atoms Mapping box atoms must be associated with a project entry the
10. To hide the toolbar Choose Toolbar from the Display menu of the main menu bar Alternatively you can type the following command into the Scripts text area or add it directly to your maestro cmd file hidepanel toolbar To hide the command input area e Choose Command Input Area from the Display menu of the main menu bar Alternatively you can type the following command into the Scripts text area or add it directly to your maestro cmd file hidepanel cominput 154 Maestro 6 5 User Manual Chapter 12 Customizing Maestro Figure 12 16 The Macros panel To Hide the clipping planes window Choose Clipping Planes Window from the Display menu of the main menu bar Alternatively you can type the following command into the Scripts text area or add it directly to your maestro cmd file hidepanel topview 12 6 Creating Macros Maestro s Macros feature allows you to assign a script command or series of commands to a particular keyboard function key F1 F12 To open the Macros panel choose Macros from the Edit menu To assign a macro to a key select the key from the Macro Key option menu and type the command or command sequence into the text area You can copy commands from the Command Script Editor panel and paste them into the text area of the Macros panel using the usual copy and paste keyboard shortcuts To test your macro click Run To save a new macro for use in subsequent Maestro sess
11. 13 2 Creating TIFF and JPEG Image Files eatem ee tert 159 Chapter 14 Job Control eere eter eese esee nese sensn senatus enata ceo nionioneo 161 14 1 Conhgunng Tob Control oi aia 161 14 1 1 The Scrateh Directory ici 161 14 1 2 Preparing for Remote Job Submission sees 162 14 1 3 Theschrodanger hosts File etes 163 14 1 4 Software Version Selection 166 14 2 Monitoring JODS 2 pec terrere Ine e dere eee Re PCR ERE RE URN E 167 14 3 Managing Jobs iio nia ca Re PETER HERE Ee RE du 169 14 3 1 Controlling Jobs From the Monitor Panel sess 169 14 3 2 Controlling Jobs From the Command Line 169 144 The Job DAADISE RE 172 144 1 The Job Record iecit ter ier e 172 144 2 Purging the Job Database 2 isis 173 14 5 Running Jobs from the Command Line eee 174 14 6 Incorporation of Job Output ciaisensis taiensis 176 Chapter 15 m ses 179 15 1 Maestro Online Help eter tenet ed eee Makes ai 179 15 1 1 Locatng Topic by Searching uccisa eas den nues 179 15 1 2 Locating a Topic by Category iui iii 180 15 1 3 Searching Within a Topic oia 180 15 2 Context Sensitive Help 181 13 3 Manuals and Release Note i 182 15 4 The Schr dinger Web Site cuina ais 182 15 5 Technical Supports e cre AIR eet e ER elisir 182 viii Maestro 6 5 User Manual
12. Chapter 3 Importing and Exporting Structures and Data Mol2 Import Sybyl Mol2 files which have a mo12 extension SD Import MDL SD files which have either a sdf extension for multiple structure files or a mol extension for files with a single structure Properties are imported as well as struc tures Babel section Import structures from a range of other programs The format conversion is performed by the program Babel The list of formats provided here is a subset of the formats that Babel can convert If you want to import structures in other formats using Babel you can use Jaguar to read the files See Section 3 1 5 on page 22 for more information You can also use Babel from the command line to convert structures to a format that Maestro can import directly To do so you must first set the environment variable BABEL_DIR csh tcsh setenv BABEL DIR SSCHRODINGER mmshare vver data babel bash ksh export BABEL _DIR SCHRODINGER mmshare vver data babel To obtain usage information enter the babel command without arguments SSCHRODINGER mmshare vver bin platform babel Here ver is the 5 digit mmshare version number and platform indicates the platform on which you are running e g linux x86 Any Import a file of any type The file type is determined from the extension of the selected file or the file name you enter in the Selection text box If the extension is not unique Maestro does not import the fi
13. Chapter 8 Projects 8 1 4 The Project Selector Panels Many of the project operations creating opening saving involve selection of a project location on disk Each of these operations has a project selector panel The project selector panels operate like file selectors but project selector filters are configured so that Maestro project directories those with prj extensions are the only visible items Most of the features of these panels are common to all operations The panel features are described below Project Availability Indicators Only one instance of a given project can be open at a time To indicate whether a project is in use an asterisk is placed in front of each avail able project and an exclamation point in front of each locked project A project is locked if you or someone else already has the project open Directory selection buttons In addition to the usual directory and file lists there are two buttons for selecting directories Launch Directory and Working Directory The first selects the directory from which Maestro was launched and the second selects Maestro s current working directory Options When you merge projects you can choose to include any user created files by selecting Include User Created Files Project Text Box The Project text box is automatically populated with the name of the current directory When you navigate to locate a directory the text box is updated to reflect Save Proje
14. Description WHICH version options LIST version options HOSTS ENTRY WHY version options Show which version of the program and of the mmshare library would be used for the given version options List the available versions of the program that can be run on the host specified by HOST If no host is specified the local host is used If version options is ALL list all available versions even if not compatible with the specified host List the hosts that are available for calculations Show the section of the schrodinger hosts file that will be used for this job Gives information about why the specified version was selected 174 Maestro 6 5 User Manual Chapter 14 Job Control Table 14 6 Version options Option Description REL version Release version number v42 v4 2 42 v42062 41059 v4 1 049 are all acceptable forms VER pattern Pattern to match in the path to the executable COMPAT executable Select the version that is compatible with the specified executable for which the full path must be given ARCH platform Platform code e g Linux x86 IRIX mips4 The allowed values of version options for the information options are listed in Table 14 6 The WAIT option All jobs are run in the background automatically dissociated from the terminal session or application from which they were launched As a result the job continues to run even if you quit Maestro or
15. HB a hydrogen on a beta carbon In these descriptions the underscore characters represent spaces which are required for compli ance with PDB semantics CA__ is a calcium atom and is different from CA 46 Maestro 6 5 User Manual Chapter 4 Building Structures Build build sj EI x AX ij ede Rf sl adah Atom Residue Properties Properties Property PDB Atom Name PDB atom name Apply PDB atom name W Pick Atoms Aan select Fragments Set unique PDB atom names within residues O Pick Residues a All Select Figure 4 10 The PDB Atom Name tools in the Atom Properties folder Occasionally when reading or writing a PDB file Maestro is not able to assign PDB names to all the atoms To manually apply missing PDB atom names enter the desired name in the PDB atom name text box and use the Apply PDB atom name picking tools to select the atoms to which you want to apply the name For some purposes such as for ligands in Prime induced fit calculations it is useful to have unique atom names within residues To make the atom names unique use the Set unique PDB atom names within residues picking tools The unique names are composed of the element symbol right justified in the first two characters followed by a numeric index for that element Grow Name This name is the name used internally for a fragment when growing a structure The intended use of this property
16. Maestro 6 5 User Manual 45 Chapter 4 Building Structures Build build si ex ARAN e ap Atom Residue Properties Properties Property Partial Charge ca Partial charge 0 0000 Solvation charge 0 0000 Fragments Apply charges partial and solvation W Pick Atoms AI Select Figure 4 9 The Partial Charge tools in the Atom Properties folder Partial Charge To apply new partial charges to atoms of interest enter new charges in the Partial Charge and Solvation Charge text boxes and use the picking tools to apply the partial charges to the atoms of interest Both of these charges are used in MacroModel calculations The solvation charge is used in MacroModel GB SA solvation calculations Generally these two values should be the same Default values for these charges are supplied with Macro Model force fields You can also use partial charges from Jaguar electrostatic potential calculations which are read by default when the results Jaguar calculations are incorpo rated or imported PDB Atom Name A PDB atom name is a combination of a chemical symbol and a connection indicator The first two characters contain the element symbol right justified the third character is a remoteness indicator A alpha B beta G gamma and so on and the fourth if it is needed is a numeric branch designator For instance the name CA represents an alpha carbon CB a beta carbon and
17. sp United atom CH sp United atom CH sp United atom CH sp Carbanion C Carbocation C Carbon free radical Any carbon Oxygen double bond Oxygen single bond United atom OH O alkoxide carboxylate United atom H O Oxonium sp 0 Oxonium sp R O Any oxygen Nitrogen sp Equivalencies MM2 MM3 Charmm Amber 2 3 CT C C C CA CB CC CM CF CG CN 1 CT CT CHIE CH CH2E C2 CH3E C3 CRIE CD CE CJ CP 30 29 T O O 02 6 OHI OH2 OS OH OHIE 47 OC OH2E 10 Maestro 6 5 User Manual Table B 1 Atom types and equivalents Continued Appendix B Atom Types No Symbol 25 N2 26 N3 27 NA 28 NB 29 NC 30 ND 31 N4 32 N5 33 NE 34 NF 35 NG 36 NH 37 NI 38 NM 39 NP 40 NO 41 H1 42 H2 43 H3 44 H4 45 H5 48 HO 49 S1 50 SA Equivalencies MM2 Description MM3 Charmm Amber Nitrogen sp 9 N NR NP N NB NC NHI NH2 N N2 Nitrogen sp 8 NH3 NT United atom NH sp United atom NH sp NHIE United atom NH sp United atom NH sp NH2E N sp NC2 NA N sp 39 N3 United atom NH sp United atom NH sp United atom NH sp NH3E United atom NH sp United atom NH5 sp NC2E N sp N sp Any nitrogen H Electroneut e g C S 5 44 HA HC HS H O Neutral 21 24 H HC HO H N Neutral 23 28 H HC H H2 H Cation 48 MM3 H3 none in MM2 H Anion Any hydrogen Sulfur 15 17 18 S S SH United atom SH SHIE
18. Color Description orange Non standard residues connected by geometry and or CONECT records Unless duplicate CONECT records are specified only single bonds are assigned so you will need to add multiple bonds red Standard residue but the input PDB file had missing atoms blue A standard residue that has some atom names unknown to the standard connec tion template The unrecognized atom names were connected by geometry green A residue with an alternate location indicator The first one listed in the PDB file is the one used to generate the converted structure gray Standard residues connected by standard templates Confidence in bond orders assigned to these residues is high Maestro imports PDB files by running a utility pdbconvert which is described in Appendix D The conversion creates a temporary Maestro formatted file and imports the structures from this file In addition to the coloring scheme which is set up in the tempo rary file Maestro displays warning messages to indicate the status of the PDB conversion which are listed in Table 3 2 Table 3 2 PDB conversion warning messages Status Message and Explanation OK No message Conversion appears successful WARNING Problems found while converting file A temporary PDB output file was generated successfully but the assignments were not all successful ERROR Could not convert file to formatname format The conversion failed usu ally because the tempo
19. Maestro 6 5 User Manual 193 Appendix B Atom Types Table B 1 Atom types and equivalents Continued 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 194 Symbol Description S thiolate anion Any Sulfur Phosphorus Boron sp Boron sp Fluorine Chlorine Bromine Iodine Silicon Dummy atom for FEP Special atom to be defined Lone electron pair Any atom Li Equivalencies MM2 MM3 Charmm Amber S 25 P 26 27 11 12 13 14 19 LP 0 Li SOD Na POT KO Rb CES CAL MG Maestro 6 5 User Manual Appendix B Atom Types Table B 1 Atom types and equivalents Continued Equivalencies MM2 No Symbol Description MM3 Charmm Amber 78 M7 Mn 79 f2 Fe 80 f3 Fe 81 02 Co 82 03 Co 83 n2 Ni 84 n3 Ni 85 cl Cu 86 c2 Cu 87 Zn Zn 88 m3 Mo 89 m4 Mo 90 m5 Mo 91 m Mo 100 SP st 10 S2 Sulfur sp 102 Cm cr CLA 150 PI Ligand dummy atom Maestro 6 5 User Manual 195 Appendix B Atom Types Table B 2 Generalized atom types No Symbol Description 151 GA Isolated atom 152 GB Linear single coordinate 153 GC Linear two coordinate 154 GD Trigonal two coordinate 155 GE Trigonal three coordinate 156 GF Tetrahedral three coordinate 157 GG Tetrahedral four coordinate 158 GH Trigonal bipyramid three coordinate 159 GI Trigonal bipyramid four coordinate 160 GJ Trigonal bipyra
20. Matching 800 atoms OK Cancel Help Figure 5 3 The Atom Selection dialog box When you are satisfied with the selection you have made click OK to apply the operation you have chosen to the selection you have made Some operations such as deleting atoms take effect immediately Others merely define a set of atoms to be used in a subsequent task such as selecting atoms for creation of a surface 5 2 1 Selecting Atoms by Property Groups of atoms that can be included in the selection are defined by a property These properties are grouped into a number of categories each in their own folder Atom Residue Molecule Chain Entry Substructure Notation and Set For each category there is a list of properties shown on the left of the folder from which you can select one item When you select an item tools specific to that property are displayed in the center of the folder The three types of tools are Text box You can specify the allowed values for the property by using lists of num bers closed ranges e g 12 42 and open ranges e g gt 30 List You can choose one or more entries from the list by clicking in combination with the SHIFT and CTRL keys Only items that are currently in the Workspace are displayed in the list Maestro 6 5 User Manual 55 Chapter 5 Selecting Atoms Set of options which can be nested You can choose only one of the possible combi nations by selecting the options For the f
21. W Display Select Entries Add Entries From Series Make Series The Selection m series X property Title X axis Title Y property SASA Y axis SASA Figure 10 5 The Series folder of the Plot Settings panel Maestro 6 5 User Manual 119 Chapter 10 Plotting Adding a Series To add another data series to the selected plot click New The New Series dialog box is displayed Select the desired values and then click New to generate a plot line for the series The controls are the same as in the New Plot dialog box see Section 10 1 on page 113 for more information Editing an Existing Series To change the settings for a series click Edit The Modify XY Data Series dialog box is displayed Modify the settings and click Edit to implement your changes The controls are the same as in the New Plot dialog box see Section 10 1 on page 113 for more information You can change all attributes of the series including the name and the data to be displayed Deleting a Series To delete the selected series click the Delete button Displaying or Undisplaying a Series To display or undisplay the selected series select or clear the Display button Adding Series Entries to the Project Table Selection Click Add Entries From Series to add entries corresponding to the selected series to the entry selection in the Project Table Making a Series the Project Table Selection To replace the entry selection in the Project Table w
22. and you must specify the entry with which the new structure should be associated Subsequent actions depend on which entry you choose If you choose one of the two source entries the other entry is deleted If you choose an existing entry other than the two source entries the new structure is added to the existing entry and the source entries are deleted The Choose Entry dialog box provides some tools for selecting the destination entry a menu to limit the entries listed and some sort options If you provide a new entry name in the Name text box the source entries are deleted and a new entry is created that contains the fused or connected structure You can undo a connect or fuse operation and the changes to the entries are also undone Choose Entry mo 0008 1 mp1 Sort 4 Alphabetically lt gt As in table Name mo 0004 imp1 Choose Cancel Figure 4 5 The Choose Entry dialog box Maestro 6 5 User Manual 41 Chapter 4 Building Structures 4 7 Adjusting the Geometry Before you use a structure for a calculation you might want to adjust the geometry espe cially if you have used Draw mode or if the Grow mode orientation was incorrect In addition to the adjustments you can make with the Move button described on page 37 you can change bond lengths bond angles dihedral angles and chirality using the tools in the Adjust panel which you open from the Edit menu in the main window or with the Dis
23. change the molecular representation in which the atoms are depicted label atoms by their properties or selectively undisplay certain atoms so that you can better examine small subsections of a structure 6 1 Changing Atom Color Changing the color of a structure can help you to visualize its properties and its three dimensional structure The Atom Coloring panel controls allow you to apply a new color to all or some of the Workspace atoms or to use predefined or user defined schemes to color specific atom groups You can also use the shortcuts available in the toolbar to change the atom coloring To open the Atom Coloring panel choose Atom Coloring from the Display menu 6 1 1 Applying a Single Color To apply a single color scheme to some or all atoms in the Workspace you can use the tools in the Atom Color folder This folder contains a color palette in the By Palette subfolder and a list of color names in the By Name subfolder You can use either of these to select a color Once you have selected a color use the picking tools in the subfolder to apply the color to selected atoms or click the All button to apply the color to all atoms in the Workspace You can also apply a color from the Color residues by constant color button menu in the toolbar This button displays a menu from which you can choose from a selection of colors The color choice is persistent You can then pick residues to apply the color or double click the
24. export E fx zonet dyall Tutorialsi Format Maestro Filter Files mdo au et build_example mae sitemap1SHD mae Directories sitemap1SHD out 1SHD prj LigPrep Qui ckTopi cs E Launch Directory Working Directory File zone1 dyall Tutorials build_example mae Append M Save graphical information Structure source to be exported lt Workspace Selected entries Files Export each entry as an individual file File names are File name entry name a Export Filter Make Directory Hide Help Figure 3 3 The Export panel 3 2 1 Selecting Export Settings The Export panel is laid out in a similar fashion to the Import panel with the file and file type selection tools at the top and various options under them Selecting a file format To create a file you must select the type of file you wish to write from the types given in the Format option menu which include Maestro MMOD Macro Model PDB Mol2 SD and a range of file types converted by Babel The file extension in most cases is determined by the file type Default file extensions for the files in the first section of the menu can be set in the File Suffix folder of the Preferences panel Properties from the Project Table are exported as well as structures to Maestro and SD files and any relevant properties are exported to PDB files Selecting a directory To select a directory you can enter it in the Path tex
25. orientation location and zoom Display only Display only the selected atoms Menu button with a list of predefined atom cat egories and an item to open the Atom Selection dialog box Undisplay Undisplay the selected atoms Menu button with a list of predefined atom cat egories and an item to open the Atom Selection dialog box Show hide or color ribbons Menu button with items to control the display of ribbons and atoms for pro teins and to color ribbons by various schemes Draw atoms in CPK Pick atoms for representation Menu button with a pick menu and an item to open the Atom Selection dialog box Draw bonds in tube Pick atoms for representation Menu button with a pick menu and an item to open the Atom Selection dialog box Color residue by constant color Pick residues to apply the selected color Double click to color all atoms Menu button with a list of colors Label picked atoms Menu button with a pick menu and items to open the Atom Selection dialog box to open the Atom Labels panel at the Composition folder and to delete labels Chapter 2 Maestro Overview Display H bonds Pick molecules to display H bonds Menu button with items to choose to display H bonds within the selected molecule intra or between the selected molecule and all other atoms in the Workspace inter or to delete H bonds 2 3 2 Shortcut Keys drals Pick atoms to define measurements Menu button with items to
26. selecting entries by 86 selecting for display 100 sorting by inedite 91 properties listing in file 205 propfalter utility nemen 204 proplister utility 205 proteins active site Mapping i 127 A alari 111 assigning secondary structure 112 atom selection examples 58 capping SIOUPSs ee 32 displaying as ribbons 65 mutating residues viewing sequence Proximity dialog box sess Q Quit panel ftdt entis 16 R rcp commard 2 rine aan 163 Read panel redeem etm 17 reference structure choosing for ePlayer 94 remote connection default commands for 163 remote hosts A sein 162 checking connection to 163 querying installation on 174 selecting for program execution 174 Settings for iii 163 166 Rename Property panel 99 residues assigning NAME eee eee eee 49 Inutating nos 35 non standard templates for 202 renumbering neneng 49 Fh stS file n x 162 Ribbon options dialog box 67 ribbons COlorSChEME sss ssscsdscssenescdesere tients display options displaying Style Maestro 6 5 User Manual rotations from superposition
27. software version command line options 175 selection by job control 166 Sort Project Table panel si 92 Spartan file format 19 spot centering on an atom 71 Maestro 6 5 User Manual Index spreadsheet exporting data to 26 importing data from 28 properties for export 100 ssh COMMANd en 163 st tus Dri etie e ee p Step mode operating ePlayer in 93 stereo viewing method specifying 146 154 structures appending to pre existing files building from fragments building in Draw mode building in Grow mode building in Place mode A ia COMMPATING seseina displaying sequentially ePlayer reference extracting by property from file extracting subset from Maestro file 203 extracting subset from SD file 204 importing multiple 20 local translations 74 O nali neret 74 submission host 165 167 substructure notation 55 96 superimposing structures 107 using the ePlayer n 94 Superposition panel en 108 S
28. tab character or choose other then enter your own delimiter in the text box Once you have made your selection click Export The file is written and its name is displayed in the Files list Export Spreadsheet exportspreadsheet EIES Path izonet dyall tutoriali Filter Files ct sx vt data txt A new csv Directories test1 csw Je Launch Directory working Directory File qikprop csw Entries am DI Properties Al a Delimiter comma o Export Filter Make Directory Hide Help Figure 3 4 The Export Spreadsheet panel Maestro 6 5 User Manual 27 Chapter 3 Importing and Exporting Structures and Data 3 4 Importing Data from a Spreadsheet Once you have exported data from Maestro and manipulated it in a spreadsheet you can re import the data into Maestro You can also import data that did not originate from Maestro Importing data from a spreadsheet file is done from the Import Spreadsheet panel and the data is added to entries in the Project Table The data that you import must therefore match entries in the project For data that you exported from Maestro matching should be no problem but for data that did not originate from Maestro you must ensure that there is a proper match to the entries in the Project Table To import data you must first open Project Table panel which you can do by choosing Show Table from the Project menu in the main window or clicking
29. ted eRe px Atom Residue Properties Properties Grow Direction forward Joining Geometry anti a Figure 4 1 The Fragments folder of the Build panel showing the Organic library If the particular fragment you want to use is not in the supplied libraries you can build it from other fragments or select a fragment with a geometry similar to the one you want to use then replace atoms with those of different elements from the Atom Properties folder The fragment libraries and grow rules are read and interpreted at run time If you are inter ested in creating your own fragments or fragment libraries please write to help schrod inger com to obtain the appropriate instructions 4 2 1 Building Structures Using Place Mode You can use Place mode to create multiple molecular structures in the Workspace to assemble structures from multiple fragments and to change a fragment into another frag ment within a structure To enter Place mode select Place in the Fragments folder To create multiple structures in the Workspace in Place mode choose a library from the Fragments option menu select a fragment and click in the Workspace Repeat this process clicking in a different place in the Workspace for each new fragment you want to place The fragments are placed in a predefined orientation at the location you select and are completed with hydrogen atoms to form molecules 34 Maestro 6 5 User
30. 208134 occ 1 00 benzene dft 01 plot a0022 MO benzene dft 01 plot a0022 MO orbital 0022 E 0 0204 occ 0 00 orbital 0022 E 0 0204 occ 0 00 benzene dft 01 plot a0023 MO benzene dft 01 plot a0023 MO orbital 0023 E 0 02047 occ 0 00 orbital 0023 E 0 02047 occ 0 00 Name 0020 E 0 203134 occ 1 00 Sort by 4 Volume lt Name Drawing Color Scheme Name Sort by 4 Volume lt Name Isovalue 0 050000 W Displayed Volume Properties D LAI Transparency Property orbital 0020 E 0 209134 occ 1 Author Jaguar Style Solid Data range 0 219464 to 0 224360 Origin 4 096699 3 761870 1 949150 Extent 8 255165 7 620152 4 021747 Resolution 39 36 19 Import Delete Limit New Import Delete Limit Hide Help Hide Help Figure 11 5 The Surface Table panel showing surface properties left and volume properties right Surface Display Surfaces are displayed when Displayed is selected in the Drawing folder To undisplay a surface deselect Displayed If the entry is not included in the Workspace the state of the Displayed option is ignored and the surface is not displayed Style and Transparency Surfaces can be displayed in three styles Solid Mesh and Dot The transparency of Solid surfaces can be changed using the Transparency slider Mesh and Dot surfaces are opaque unless the Transparency slider is set to 100 when t
31. 45 46 47 48 Fragments folder 34 35 Residue Properties folder button menu iii C Calculate Properties panel centroid defining Centroids panel siria ChainmamMEes siii charges assigning i Choose Entry dialog bOX Choose Import Key dialog box 29 clipping planes window T hiding and redisplaying ES S 211 Index color schemes atom labels tees 68 AMS cup deett 59 61 FIDDONS paria 66 SUI TAGES ila lai 134 Workspace background 146 Command Aliases panel 150 command aliases creating 150 command hiStory ie 151 command input area in 7 Md crisi 154 command options jaguar run 174 Command Script Editor panel 151 command scripts 151 155 customizing Maestro with 153 running with ePlayer 95 compressing MacroModel files 199 Connect amp Fuse panel 40 connectivity template for pdbconvert 202 Connolly surface sese 125 contacts criteria dotan 106 displaying Continuous mode operating ePlayer in 93 conventions documenti 1 entry DAMS 22 entry renaming eee 177 197 conver
32. Building Structures 52 Maestro 6 5 User Manual Chapter 5 Selecting Atoms Maestro has a powerful set of tools for selecting or picking atoms in a Workspace struc ture that takes advantage of chemical information about the structure These picking tools are embedded in each panel in which you need to select atoms to apply an operation The picking tools in a panel can include one or more of a Pick menu an All button a Select button which opens the Atom Selection dialog box an ASL text box a Clear button and a Show markers option ASL stands for Atom Specification Language and is described in detail in the Maestro Command Reference Manual Pick menus are also included in some toolbar button menus The range of picking tools available in a panel varies according to the types of structural unit that are needed for the operation and to whether picking causes immediate action or requires an action to be specified later The ASL text box and Clear button are included only when picking merely defines a set of atoms for later use For example the Label Atoms section of the Atom Labels panel has a Pick menu an All button and a Select button and the action is immediate The Sets panel has a full set of picking tools and stores the atoms in a defined set that can be used later 5 1 The Pick Menu The simplest form of atom selection involves selection of an object from a Pick menu and clicking on an atom or a bond in the Workspace The obje
33. Help Figure 9 2 The H Bonds and Contacts folders of the Measurements panel Maestro 6 5 User Manual 105 Chapter 9 Tools In order to see hydrogen bonds or contacts marked in the Workspace you must select Display H bonds or Display Contacts In addition to display contacts you must select the type of contact Good Bad or Ugly that you want to measure Default criteria for defining hydrogen bonds or contacts are given in the text boxes at the top of the folder To change these criteria enter a new value in the relevant text box For hydrogen bonds you can set the Maximum distance Minimum donor angle and Minimum acceptor angle For contacts you can alter the contact cutoff ratios in the Good contacts Bad contacts or Ugly contacts text boxes To define an atom set use the picking tools click Select to open the Atom Selection dialog box or enter an ASL expression in the ASL text box If you define only Atom set 1 the H bonds or contacts are displayed within that set If you define both Atom set 1 and Atom set 2 the H bonds or contacts are displayed between the two sets When you have finished measuring click Clear in each of the atom definition sections You can also display hydrogen bonds from the toolbar First select Inter H bonds or Intra H bonds from the Display H bonds button menu al Then pick a molecule in the Workspace If you selected Inter H bonds hydrogen bonds between the selected molecule and the
34. Maestro 6 5 User Manual 173 Chapter 14 Job Control The minimum time is 1 second and the default time is 1 week The default unit is seconds but you can specify a time in minutes hours or days by appending m h or d to the value for example 7d 168h or 5m 14 5 Running Jobs from the Command Line For most purposes you can start jobs from Maestro If you want to run jobs from the command line or from a script the job control facility recognizes a number of command line options that can be used to control the behavior of the job These options are summa rized in Table 14 4 Some of the options are described in more detail below Table 14 4 Command options Option Effect Default Behavior HOST Run a job on the specified host or submit Run on the local host hostname a job to the specified batch queue LOCAL Write temporary files to the job startup Write temporary files to the scratch directory instead of the scratch directory directory USER Specify the user name to be used for Use the same user name as on the username remote jobs Must be used with HOST job submission host WAIT Wait for the job to finish before returning Return to the command prompt to the command prompt Replaces w immediately You can also obtain information for each program about the hosts you can use and which version of the program will be run These options are listed in Table 14 5 Table 14 5 Information options Option
35. Most of the windows that are opened from Maestro are amodal and are called panels More than one panel can be open at any given time and a panel need not be closed for an action to be carried out Panels are closed by clicking the Hide button This button replaces the Close button or the Close menu item found in other interfaces Maestro also has dialog boxes which are modal they must be closed before you can carry out an action in any other panel Dialog boxes must be closed for the action to be carried out Some dialog boxes allow you to carry out limited operations in other panels such as the Workspace and some dialog boxes allow you to open the help viewer so that you can obtain information about the dialog box 2 2 2 Mouse Functions The mouse functions that are common to graphical user interfaces are supported in Maestro e The left button is used for selecting choosing menu items clicking buttons and selecting objects This button is also used for resizing and moving panels In the description of mouse actions click always means left click The right button is used for opening a context sensitive menu where these menus are available Shift click is used to select a contiguous range of items in a list and control click is used to select and deselect a single item in a list without affecting the selection of other items Dragging operations are supported For example in the Project Table dragging selected entries
36. Pg 50 4 12 Sle tne OMS nacio 51 Chapter 5 Selecting Atoms coron rone etae eoa ee ean aer sere Un e ene oe eene 53 5 1 The Pick Mentee cove 53 5 2 The Atom Selection Dialog BOX ire 54 3 2 1 Selecting Atoms by Property iio iii did 55 5 2 2 Combining and Modifying Atom Selections sss 56 5 2 3 Selecting Atoms by Proximity ts cpcece sla gies eh deena 56 5 2 4 Editing and Storing ExpressIOs 5 ceteri e eerie in 57 5 2 5 Exartiples of Atom Selection alii 57 Chapter 6 Displaying Structures e eee crescere ee ee ette seen etes eene etn ssennionee 59 6 1 Changping Aton Color e eee eon ee dee e HS 59 6 1 1 Applying a Single COlOr ue 59 6 1 2 Using Predefined Schemes to Color Atoms iii 61 6 2 Changing Molecular Representations esee 61 6 2 1 Changing the Representation of Atoms 61 6 2 2 Changing the Representation of Bonds 55 eee 62 6 2 3 Changing Representation Attributes 64 6 2 4 Rendering Proteins s Ribbons ence tette 65 6 3 Labeling AOS vans ii Ai ii e ADEL 67 6 4 Displaying and Undisplaying AtomS i 69 Chapter 7 Manipulating Struciures cssesssevosossssessiseesesssesessassscve sessuosussssossssu o 71 1 1 Global Transtormations ss senado sissi nisso toi 71 1 2 Local TEAMSTOMMANONS lia i 72 7 2 1 Selecting A
37. Specified then click the Specify button The User Specified Conflict Resolution panel is displayed and you can choose to rename either the current or the incoming entry The resolution scheme that Maestro offers may not produce especially meaningful names For example if in both the current and the merge source project you have entries named entry and you already have other entries in the current project named entry 1 entry 2 and entry 3 Maestro renames the incoming entry as entry 4 Since renaming entries in this fashion may destroy any location cues that you were using you may want to go into each project separately and resolve any naming conflicts before attempting to merge projects However the titles of the entries are preserved and these can be used to distinguish entries when the entry name is changed by Maestro 8 3 The Project Table Panel The Project Table panel provides access to a range of tools for managing the data in the project and operating on that data The panel contains a menu bar a toolbar and the Project Table itself This section provides a brief description of the basic table operations the tools and the use of the mouse and shortcut keys for performing various operations Each project entry is represented by a row in the Project Table Each row contains the row number an icon in the In column indicating whether the entry is displayed in the Work space the title a button to open the Surfaces panel if there a
38. The exception is measurement markers which are displayed even if the Measurements panel is hidden You can set preferences for when markers are deleted in the Delete Markers folder of the Preferences panel See Section 12 2 1 on page 138 for more information To display the markers for a particular operation select Show Markers in the panel used to perform the operation 9 2 Making Measurements in the Workspace The Measurements panel provides tools to determine the geometric relationships between atoms in the Workspace These tools are contained in five folders Distances Angles Dihedrals H Bonds and Contacts To open the Measurements panel choose Measurements from the Analysis menu 9 2 4 Measuring Distances Angles and Dihedrals The controls for Distances Angles and Dihedrals are very similar as are the actual measurement procedures for these quantities To measure a distance you need to specify only two atoms or one bond for an angle you must specify three atoms or two bonds and for dihedrals you must specify four atoms or three bonds Maestro 6 5 User Manual 103 Chapter 9 Tools asurements measurements IE xi Distances Angles Dihedrals H Bonds Contacts 4 Add Q Delete Define atoms for distance measurement W Pick Atoms WE Show markers Atom Atom2 Distance 1 780 33 32 2 467 i Delete Delete All Write LI Create property for selected entries Hid
39. W Auto range ew Edit Delete W Display W Auto range Title Title Title SASA Minimum 1 000000 Minimum 250 000000 Maximum 20 000000 Maximum 1000 000000 Number of scale markers Low Number of Scale Markers Low Figure 10 6 The X Axis and Y Axis folders of the Plot Settings panel Setting the Axis Range To set the axis range to the combined range of all the data series select Auto range To set the range manually deselect Auto range click Edit and set the range 10 4 Updating Plots to Reflect Project Table Changes If the data values in the Project Table that are used for a plot have changed you can update the plot with the new values by choosing Update Selected Plots from the Plot menu For example if you run a job with Replace selected some cells in the table may acquire new values If you want these values to replace old values in a plot select the plot then use the Update Selected Plots command Maestro 6 5 User Manual 121 Chapter 10 Plotting Save PlotXY Image plotxysavel IE X Image format 4 TIFF lt gt JPEG Save Save To Hide Help Figure 10 7 The Save PlotXY Image panel 10 5 Saving Plot Images The Save PlotXY Image panel is used to save an image of the plotting panel to a file To open the Save PlotXY Image panel choose Save PlotXY Image from the Plot menu Saved images have the same dimensions in pixels as the Plot XY panel For images to sav
40. allows you to reposition the entries dragging a column heading moves the column dragging with the middle mouse button on the boundary of a row or column resizes the row or column If you have the handedness on your mouse set to left the mouse functions are the mirror image of those described the right mouse button is used for picking and the left button is used for context sensitive menus If you have a two button mouse ensure that it is configured for three button mouse simu lation Then the middle mouse button is simulated by pressing or holding down both buttons The Workspace has special uses for the middle and right mouse buttons These are used on their own and in combination with the SHIFT and CTRL keys to perform common opera tions such as rotation translation centering and zooming See Chapter 7 for more infor mation Maestro 6 5 User Manual 5 Chapter 2 Maestro Overview 2 3 The Maestro Main Window The Maestro main window is shown in Figure 2 1 The main window components are as follows Title bar displays the project name and the current working directory Auto Help automatically displays context sensitive help Main menu bar provides access to panels Workspace displays molecular structures Title bar Auto Help text area Main menu bar Workspace maestro zonel dyall Tutorials QuickTopics Pick pairs of atoms which define the supe imposition Project Edit Display Tools Application
41. as a PDB file that does not have explicit hydrogens present Adjust Bond Lengths When Atom Type Is Changed When atom types are changed bond lengths are automatically adjusted to give a reason able bond length This behavior is undesirable if the geometry is already correct such as from a crystal structure and it is only necessary to change the atom types Deselecting this option prevents the adjustment of bond lengths 144 Maestro 6 5 User Manual Chapter 12 Customizing Maestro Adjust Number Of Hydrogens During Build Operations The number of hydrogen atoms is adjusted by default to maintain a normal valence during formal charge bond order or retyping changes This behavior is not always desirable and can be prevented by deselecting this option Delete Terminal Atoms When you delete an atom the terminal atoms that are attached to this atom can be deleted or they can be left in place Terminal atoms are atoms that are bonded only to that atom such as hydrogen or a halogen Deleting terminal atoms would not for example delete a methyl group attached to the deleted atom 12 3 Customizing the Workspace The Display Options panel contains controls for setting the background color of the Work space and for selecting 3D viewing options The Display menu also has options for showing or hiding Workspace controls and displays To open the Display Options panel choose Display Options from the Display menu of the Main Menu
42. assigning 49 pdbconvert utility in 200 Perspective folder e 147 perspective enabling 147 154 Pick Me NUS iine uro rre dn 53 PICK state cid 7 54 Place mode building in 34 35 Plot Settings panel Plot folder iia iaa 118 Series folder oae ina 119 X Axis Toldos ias 121 Y Axis fold r aa ether nete 121 Plot XY panel eet ener LIS plots adding data series t0 119 axis displasia 120 eru Me LIS deselecting entries from 117 editing datd cir 119 excluding entries from 117 file formats cassa aries 122 including entries from 117 labeling data points 116 line frequency ohne 113 modifying attributes 118 panning and zooming 116 DX ils asas cera 122 selecting eec eet LIS selecting entries from 117 120 updating from project table 121 VICWINS ecco aieo ds 114 215 Index preferences file S ffX iia 143 TOHUSIZe a uota re eS 138 Marker EO 138 MU n 142 S INE ripiano ear 137 synchronization 95 139 working directory usse 141 preferences directory sess 137 Preferences panel Builder fol
43. atom You can choose from All Attached Atoms All Attached Terminal Atoms or Only Single Atom If the target atom is part of a ring the first of these options is unavailable To make the adjustment you can enter a new value for the geometric parameter in the text box or you can use the mouse If you enter a new value the value is changed and the Workspace updated when you press ENTER To adjust the geometry using the mouse select Allow Adjustment then drag with the middle mouse button to adjust the geometry To adjust the stereochemistry at a chiral center use the picking tools in the Chirality folder You can invert the chirality of selected chiral centers or of all chiral centers This folder also has buttons for displaying the R and S labels for the configuration at chiral centers and for clearing the labels If you click Label Chiral Centers all other labels are cleared 4 8 Applying a Hydrogen Treatment When building molecules or preparing proteins you might want to apply a hydrogen treat ment that is compatible with the force field you intend to use in calculations on those structures You can also use a hydrogen treatment to add hydrogen atoms to a structure that is used for any program that requires explicit hydrogen atoms such as QikProp and Jaguar Hydrogen treatments can treat hydrogen atoms explicitly or implicitly as part of another atom To select and apply a hydrogen treatment you can use the controls in the Hydrogen Tre
44. bipyridyl from two pyridine rings by connecting the 2 carbon on one ring with the 5 carbon on the other and deleting the hydrogen atoms Fusing two structures deletes atoms An example is the fusion of two benzene rings in which two carbon and two hydrogen atoms are deleted from one ring and bonds formed to the other ring with deletion of two hydrogen atoms The tools for fusing and connecting structures are available from the Connect amp Fuse panel In the connection and fusion operations an attempt is made to create structures with reasonable geometries and a check is made that valency is not violated This is in contrast to Draw mode which does not evaluate bonding or geometry For both connect and fuse operations you must first select atom pairs to be joined The atoms you select must not be hydrogen atoms You can select as many pairs as you like The first atoms in all selected pairs must all come from the same molecule and the second atoms in the pairs must come from the same molecule The molecule for the set of first atoms set need not be different from the molecule for the set of second atoms If you select a pair of atoms in the same molecule a new bond is drawn between the atoms To select atoms for a connect or fuse operation ensure that Pick to define atom pairs is selected and click on the Workspace atoms to define the pairs Atom numbers of the selected pairs appear in the Connect or fuse atoms list Also if Show Markers i
45. box or click All You can apply the current scheme to all existing ribbons by clicking Update Existing Ribbons If you want to change the scheme for a part of the protein or for one existing ribbon rather than all ribbons use the tools in the Apply Ribbons to Atoms section The display options in the lower part of the folder allow you to display the ribbons only the atoms only or both The atom display operates only on the already displayed atoms and only on the atoms for which a ribbon is defined 66 Maestro 6 5 User Manual Chapter 6 Displaying Structures Ribbon options Quality steps ATT 1 30 Ribbon width A Ribbon thickness A Strand width A Strand thickness A Thin tube width A Thick tube width A Restore Defaults OK Cancel Figure 6 7 The Ribbon options dialog box You can apply the color schemes and the display options using the Show hide or color ribbons toolbar button menu If you want to change the quality of the ribbons or the width or thickness of the ribbons strands or tubes click Settings The Ribbon options dialog box is displayed This dialog box has slider controls for quality ribbon width ribbon thickness strand width strand thickness thin tube width and thick tube width and a button to restore the default values 6 3 Labeling Atoms Labels are useful tools for building identifying and analyzing molecular structures since they ca
46. button to apply the color to all atoms If the color you want to use is not on the menu you can use the Atom Color folder to select the color Maestro 6 5 User Manual 59 Chapter 6 Displaying Structures om Coloring col tom Coloring coloratom Color Scheme Atom Color Color Scheme Atom Color By Palette By Name By Palette By Name Atom color Atom color black blue blue purple blue1 blue2 blue3 blue4 blues NE blue blue blues blues Apply current color Apply current color W Pick Atoms Select W Pick Atoms Select Figure 6 1 The By Palette and By Name folders of the Atom Coloring panel m Coloring Color Scheme Atom Color Legend for Element Color Element white Hydrogen H green Boron B gray Carbon C blue Nitrogen N red Oxygen 0 aquamarine Fluorine F orange Silicon Si maroon Phosphorus P yellow Sulfur S dark green Chlorine Cl lement Entry Entry Carbons Molecule Number Molecule Number Carbons Apply current color scheme W Pick Atoms Figure 6 2 The Color Scheme folder of the Atom Coloring panel 60 Maestro 6 5 User Manual Chapter 6 Displaying Structures 6 1 2 Using Predefined Schemes to Color Atoms To apply coloring to some or all Workspace atoms using one of Maestro s predefined color schemes you can use the tools in the Color Scheme folder Click on the desired scheme name in the list in
47. can restrict or enhance your search by selecting the following options Title Only The search is restricted to the topic titles Case Sensitive The case is matched exactly in the search Regular Expression Allows the use of UNIX regular expressions in the search Maestro 6 5 User Manual 179 Chapter 15 Help Help help Ge Search Categories Search for Title only L Case sensitive LI Regular expression Topics which match search double click to view Adding Workspace Entries to the Selection Atom Specification Language CASL Edit Filter Panel Topic Help Panel Contents e Summary Opening the Help panel e Search Methods e Restricting Your Search e Help Panel Features Summary Search current topic for Next J Case sensitive Hide Help Figure 15 1 The Help panel showing the Search folder 15 1 2 Locating a Topic by Category Searching for help by category is helpful when you do not know which keywords may produce the desired topic Select the option from the Help Categories menu that corre sponds to the group of topics you would like to browse A list of relevant topics is displayed in the Topics in this category list The topics in the list are arranged in alphabet ical order and the last entry in the list is highlighted To select a topic double click its name or click its name and press RETURN 15 1 3 Searching Within a Topic If you want to locate a string in the to
48. changes to Redo once you have used it 14 Maestro 6 5 User Manual Chapter 2 Maestro Overview Maestro itself can perform certain actions such as job monitoring from within undo blocks These actions might prevent the entire sequence of operations from being undone 2 7 2 Undoing Operations on the View Global molecular transformations such as rotations and translations cannot be undone with the Undo option on the Edit menu or in Undo Blocks To undo such a transformation you must save the orientation of the structure before you do the global transformation You can also revert to the default orientation and zoom The default orientation is defined by the coordinates of the structure The default zoom value is the value you get by clicking the Fit to screen button on the toolbar To save an orientation e Click the Save view button in the toolbar y TD To restore the saved orientation Click the Restore view button in the toolbar To revert to the default orientation and zoom Click the Reset workspace button in the toolbar de XYZ 2 8 Ending a Maestro Session To end a Maestro session choose Quit from the Maestro menu If you would like to save a log file with a record of all operations performed in the current session click Quit save log file on the Quit panel This information can be useful to Schr dinger support staff when responding to any problem you report If you do not want to save a log file c
49. choose between distance default angle or dihedral measurement and to delete measurements Measure distances angles or dihe Some frequently used operations in the main window have been assigned shortcut key combinations The shortcuts their functions and their menu equivalents are listed in Table 2 2 Shortcut keys in the Project Table panel and the Plot panel are listed in the chap ters that describe those panels Table 2 2 Shortcut keys in the Maestro main window Keys Action Equivalent Menu Choice ALT B Show build panel Edit gt Build ALT C Create entry Project gt Create Entry From Workspace ALT E Show script panel Edit gt Command Script Editor ALT H Show help panel Help gt Help ALT I Show import panel Project gt Import Structures ALT M Show measurement panel Analysis gt Measurement ALT N New project Project gt New Project ALT O Open project Project gt Open Project ALT P Print Maestro gt Print ALT Q Quit Maestro gt Quit ALT S Show sets panel Analysis gt Sets ALT T Show project table panel Project gt Show Table ALT W Close project Project gt Close Project ALT Z Undo Redo last command Edit gt Undo Redo 10 Maestro 6 5 User Manual Chapter 2 Maestro Overview 2 4 Maestro Workflow For most operations that you perform in Maestro you must first define or choose an action then choose the atoms to which the action will be applied For example to change the color of all atoms in
50. command line 14 3 1 Controlling Jobs From the Monitor Panel The Monitor panel allows jobs to be paused resumed or terminated using the Pause Resume Stop and Kill buttons Clicking Kill terminates the selected computational job immediately The Stop button only affects MacroModel and Jaguar jobs and is ignored by other jobs When a job is stopped the program saves results from the current stage of execution and cleans up before exiting Pause and Resume can be used for all jobs 14 3 2 Controlling Jobs From the Command Line The job control utility allows you to perform a number of job control tasks from the command line The syntax for job control utility commands is SCHRODINGER jobcontrol command job selection where command is the command for the operation you want to perform and job selection is the name of the specific job if applicable Valid commands are listed in Table 14 2 The optional job selection consists of one or more Joblds job names status codes or queries or the keywords all or active The default job selection is all active jobs jobs that are not finished and is equivalent to using the keyword active The keyword all means all jobs in your job database The Jobld is a unique identifier consisting of the name Maestro 6 5 User Manual 169 Chapter 14 Job Control Table 14 2 Jobcontrol commands Command Action cancel cancel a job that has been launched but not started delete remove a complet
51. curved line that follows the backbone CA Trace straight line that connects alpha carbon atoms CA Trace Tube straight tube that connects alpha carbon atoms Maestro 6 5 User Manual 65 Chapter 6 Displaying Structures Molecular Representation rep EEE Settings Atoms Bonds Ribbons Style Cartoon E Color scheme Secondary Structure Constant color Update Existing Ribbons Apply ribbons to atoms W Pick Chains an select Display 4 Ribbons only Atoms only Both Helices lt One color 4 Two colors Delete All Ribbons Settings Figure 6 6 The Ribbons folder of the Molecular Representation panel With the exception of the CA Atom Color scheme the color schemes are described in the Color Scheme folder of the Atom Coloring panel In the CA Atom Color scheme the ribbon is colored with the current color of the alpha carbon atoms Thus if you change the color of certain residues and reapply this color scheme the section of the ribbon for which you changed the residue color changes color to match You can also select a two color repre sentation of helices using the Helices options in the lower part of the panel The chosen color scheme is applied to the outside of the helix and the inside of the helix is gray To apply the chosen style and color scheme you can use the picking tools in the Apply Ribbons To Atoms section or click Select to use the Atom Selection dialog
52. define an Undo block before starting the superposition For more information on Undo blocks see Section 2 7 1 on page 14 You can store the RMS deviation as a property for each entry that was superimposed To create a property select Create property for included entries before you perform the super position The property is labeled RMSD entry name or RMSD In Place entry name depending on how you performed the superposition The reference entry has a value of Zero for this property The reference entry name is used for entry name in the label If you change the details of the superposition but do not change the reference entry the property values are replaced You can always rename the property if you want to keep the property and perform other superpositions with the same reference entry See Section 8 7 3 on page 99 for information on renaming properties 94 Sets Sets are groups of atoms that can be used in a variety of Maestro operations The Sets Panel is used to define these atom groups for subsequent operations and can be used to save and read set definitions To open the Sets panel choose Sets from the Tools menu 9 4 1 Creating and Deleting Sets To create a new set click the New button In the dialog box that appears enter a name for the set and click OK This name is used to identify the set in later operations The name is added to the list at the top of the Sets panel To delete a set select the set name in the set list
53. enter any data in the section below the list select a Calculate For Entries option All or Selected then click Calculate 96 Maestro 6 5 User Manual Chapter 8 Projects Calculate Properties calcprop EEE Number of atoms Number of residues Number of molecules Molecular weight r formula Molecular charge Secondary Structure Content Molecular formula Ignore entries with more than 100 atoms Calculate for entries gt All 4 Selected _ Recalculate existing values Calculate Hide Help Figure 8 8 The Calculate Properties panel If you have previously calculated the property for some entries and want to calculate it for other entries you can choose to recalculate the existing values by selecting Recalculate existing values 8 7 2 Changing Property Values Maestro provides several means of changing the values of properties You can edit indi vidual cells and the selected cells of a single column and you can copy values from another property To edit the contents of an individual Project Table cell click the cell edit the contents then press ENTER or click elsewhere in the Project Table If the cell is not in a selected entry the entry it is in is selected and all others are deselected To set the value of a property to a particular value for the selected entries click one of the cells edit the contents then press CTRL ENTER The new value is copied to all selected entries You can copy and pa
54. for ligand molecules can also be created To specify a template file to be used by pdbconvert use the data option The standard residue template file for pdbconvert can be viewed at SCHRODINGER mmshare vversion data mmpdb ini D 1 4 Conversions to and From SD Format sdconvert Convert between MDL SD Maestro and MacroModel format files Syntax sdconvert options isd imm imae inputfile osd omm omae outputfile isd Input file in SDfile format imm Input file in MacroModel format imae Input file in Maestro format osd Output file in SDfile format omm Output file in MacroModel format omae Output file in Maestro format 202 Maestro 6 5 User Manual Appendix D Utilities Options a Append structures to the output file all Convert all structures synonym for n 1 This is the default action h Show usage summary n structs Specify a comma delimited series of colon separated ranges and single values to convert For example 1 10 14 structures 1 through 10 and 14 23 structure 2 through end of file 5 13 18 structure 1 through 5 and 13 through 18 For multiple n options the right most takes precedence Example SSCHRODINGER utilities sdconvert n 1 isd lig sdf omae lig mae D 2 Structure Extraction This section describes utilities for extracting a subset of structures from a structure file The first two utilities maesubset and sdsubset extract structures by index The third util
55. for plot output 122 fragment libraries inn 32 34 Fragment mode building structures in 32 fragments BOON ciar tende 32 34 building with sees 32 connecting and fusing 40 specifying growth settings for 36 frequency pIots ie 113 G global transformations e 7l switching t0 ine 73 STOW DONG iii ida 36 209 Grow mode building in 36 growth settings specifying 36 H help Auto Help Balloon help online Help panel Categories folder Search folder hetero atoms labeling 213 Index hosts ACCESS O iia id 162 checking connection to 163 database settings 163 166 querying installation on 174 selecting for program execution 174 hosts equayv file nee 162 hydrogen bonds Criterl Tor ias 106 display iria nin 105 hydrogen treatment applying eene 43 206 force field compatibility 44 Hydrogen Treatment panel 43 hydrophobic and hydrophilic regions displaying eie creer 127 I image output PostScript and EPS files 157 TIFF and JPEG files image quality JPEG files surfaces Importpanel a u eicere mes Import Spreadsheet panel 28 imp
56. from Workspace 79 deleti eerte mrs 91 displaying in Workspace 89 duplicating nr ite 90 excludirig int ia na dii 89 excluding using plots a 117 Import ici ria 78 INCIUGING isc ritos 89 including using plots 117 incorporating from job output 79 METIO is 79 merging on connection or fusion 41 MOVIN E csi ati 91 name conflict resolution 79 properties tenes 95 101 TODAS ciccia ca iii 89 renaming conventions for 177 197 Maestro 6 5 User Manual A sasncies 85 89 selecting from plots 117 120 A eroe eee tard 81 91 splitting by molecule 90 SUARES ciebat n ains 197 superimposing iii 107 Mi ias 74 See also properties of entries Entry Selection dialog box 87 Entry Selection Language ESL 86 environment variables BABEL DIR soria ross 19 DIS PLAY pisani irta 3 SCHRODINGER 22 eer eene snot hoan 3 SCHRODINGER HOSTS 163 SCHRODINGER JOBDB CLEANUP 173 SCHRODINGER RCP 163 SCHRODINGER RSH 163 SCHRODINGER TMPDIR 162 165 TEMP PROJECT tdi 75 TMPDIR sonatas 162 CPLA EI ini 92 95 reference StrUCture 94 speed isset 94 toolbar controls eese 82 ePlayer Options panel 94 error codes pdbc
57. is labeling new fragments for a fragment library Atom Name You can assign one of three types of names to atoms in the Workspace user specified canonical or unique User specified names can be any length To assign a user specified Maestro 6 5 User Manual 47 Chapter 4 Building Structures Build build si ex ARA eGR ade Atom Residue Properties Properties Fragments Property Atom Name A Set atom name Atom name W Pick Atoms All Canonical names Composition Element amp Atom Number a Separator Apply To All Atoms Modify existing names Make Unique Figure 4 11 The Atom Name tools in the Atom Properties folder name type the desired name in the Atom name text box of the Set atom name section and use the picking tools to apply the name You must display the atom name labels before you can see the new name A canonical atom name is an automatically assigned combination of atom property pairs Element amp Atom Number or Residue Number amp PDB Atom Name To assign canonical names select the desired pair of properties from the Composition option menu specify a separator symbol in the Separator text box and click Apply To All Atoms You cannot selectively apply canonical names Unique names are generated using the element and atom number of each atom If this naming scheme produces atoms with identical names Maestro adds numeric suffixes followed by tild
58. located in the Project Table panel Maestro 6 5 User Manual 209 Glossary selection 1 A group of atoms in the Workspace that has been picked or otherwise chosen The selection is highlighted by markers when the appropriate option is selected 2 A group of entries in the Project Table The entries are highlighted in the table synchronization updating the project with changes made in the Workspace The default is to perform synchronizations automatically volume a set of data points on a three dimensional grid for a property that is a function of the three spatial coordinates Workspace The open area in the center of the Maestro main window in which structures are displayed 210 Maestro 6 5 User Manual Index Numerics ID Merino eh 146 A active atom changing iii 37 Add Property panel in 96 Adjust panel eer errem 42 Advanced Transformations panel 73 Openpolis 72 allas iia ins 150 angles Measuring iii 103 ASD iaa its 209 AS BRR ERR e A ias 209 Atom Coloring panel e 60 OPIO Picar iioii 39 atom labels adding user text tO eects 68 APP ira 69 applying while building 32 Coloring iia 141 composing 67 hetero atoms e 68 including descriptions in 142 AAA ea a 141 removing si 09 updating sa 09 Atom Labels panel
59. must replace with a value Sans serif ALT H Keyboard keys uppercase The use of this version of Maestro should be cited in publications as Maestro 6 5 Schr dinger LLC Portland OR 1999 2004 Maestro 6 5 User Manual 1 Chapter 1 Document Overview 2 Maestro 6 5 User Manual Chapter 2 Maestro Overview Maestro is the graphical user interface GUI for all of Schr dinger s computational programs FirstDiscovery Glide Impact Liaison QSite Jaguar LigPrep MacroModel Prime and QikProp It contains tools for building displaying and manipulating chemical structures for organizing loading and storing these structures and associated data and for setting up submitting monitoring and visualizing the results of calculations on these structures Maestro s job control facility manages jobs submitted from Maestro and from the command line to both local and remote hosts The Maestro interface uses the OpenGL graphics tools and can take advantage of hard ware graphics capabilities including stereo viewing capabilities Maestro runs on SGI and Linux platforms For information on Maestro requirements software and hardware see the Schr dinger Product Installation Guide For information on configuring stereo viewing see Section 12 3 on page 145 This chapter provides an overview of Maestro the general interface design starting and ending a Maestro session the main window and its features Maestro
60. n instead of simply n where n is the number of the molecule 12 2 6 Setting Mouse Preferences If you want to change the sensitivity of rotation of Workspace structures to mouse move ment use the Sensitivity in rotation slider in the Mouse folder to adjust the sensitivity Increasing mouse sensitivity means that moving the mouse results in greater movement of the molecule in the Workspace You can choose whether or not audio feedback is given when you use the mouse to pick atoms in the Workspace By default Beep when picking is selected 142 Maestro 6 5 User Manual Chapter 12 Customizing Maestro Preferences prefer Delete Markers Font size Project Directory Label Mouse File suffix Builder 75 mm Sensitivity in rotation W Beep when picking Figure 12 6 The Mouse folder of the Preferences panel 12 2 7 Setting File Suffix Preferences You can change the default file suffixes that are used for the file types that Maestro recog nizes in the File Suffix folder These suffixes are appended to file names when you export structures using the Export panel These file suffixes do not include suffixes for file formats converted by Babel Preferences prefer Delete Markers Font size Project Directory Label Mouse File Suffix Builder Maestro mae Macromodel dat PDB pdb Mol2 mol2 SD sdf Restore Defaults Figure 12 7 The File Suffix folder of the Preferences panel Mae
61. of a job is displayed as the job s Status in the Monitor panel The Status of a completed job indicates the conditions under which it stopped The job status descriptors that can appear in the Monitor panel are listed in Table 14 1 Table 14 1 Status descriptors in the Monitor panel Status Meaning launched The job was submitted and assigned a Jobld submitted The job is in a batch queue waiting to be scheduled started The environment for the job is being set up running The job is running paused The job has temporarily been suspended exited The job has exited and is being cleaned up finished The job finished successfully 168 Maestro 6 5 User Manual Chapter 14 Job Control Table 14 1 Status descriptors in the Monitor panel Continued Status Meaning stopped The job was stopped at an appropriate point at the user s request killed The job was killed by someone not necessarily the user died The job failed during execution incorporated The job results have been incorporated into a Maestro project fizzled The job failed before it could be started stranded Job control could not retrieve results or clean up the job unreachable Job control could not connect to the machine running the job 14 3 Managing Jobs You can manage or control jobs from the Monitor panel or from the command line The common tasks can be performed from the Monitor panel but the full range of job control tasks is only available from the
62. plane camera The perspective controls are in the Perspective subfolder of the 3D folder You can adjust the scaling using the Perspective Scale slider The green lines in the Top View window move to reflect the viewing volume available at a given value on the Perspective Scale 12 3 5 Enabling Fog Maestro s Fog feature causes atom colors in the displayed structure to fade toward that of the background as atom coordinates grow increasingly negative in the z direction This feature is particularly useful for depth cueing when viewing large structures such as proteins and when using the Wire molecular representation The fog controls are in the Fog subfolder of the 3D folder Fogging is turned off by default To enable fogging select On or Automatic from the Display Fog option menu Automatic fogging means that fogging is turned on when a molecule is bigger than a given number of atoms Below this threshold fogging is turned off The threshold is 40 atoms and can be Maestro 6 5 User Manual 147 Chapter 12 Customizing Maestro Display Options displayopt lei Background 3D Stereo Perspective Fog LI Display in perspective 1 50 MT ig amp ug lff Perspective scale normal 1 5 Alignment depth W Adjust clipping to preserve depth cues Enhance Depth Cues Figure 12 11 The Perspective folder of the Display Options panel set with the Maestro command displayopt fogcutoff number You can indepen
63. projects and work flow and running jobs from Maestro 2 1 Starting Maestro Before you start Maestro you must set the SCHRODINGER environment variable to point to the installation directory You can set this variable by entering the following command at a shell prompt csh tesh setenv SCHRODINGER installation directory bash ksh export SCHRODINGER installation directory You might also need to set the DISPLAY environment variable if it is not set automatically when you log in To determine if you need to set this variable enter the command echo SDISPLAY Tf the response is a blank line set the variable by entering the following command csh tesh setenv DISPLAY display machine name 0 0 bash ksh export DISPLAY display machine name 0 0 After you set the SCHRODINGER and DISPLAY environment variables you can start Maestro using the command SSCHRODINGER maestro options filename Maestro 6 5 User Manual 3 Chapter 2 Maestro Overview The options for the maestro command are listed in Table 2 1 The optional filename specifies a file in Maestro or MacroModel format Table 2 1 Options for the maestro command Option Description b PDB file Read a PDB file Cannot be used with m c command script Run the specified Maestro command script when Maestro starts h Print a usage message but do not start Maestro m filename Load structures from a Maestro mae or MacroModel dat struc ture file C
64. rest of the atoms in the Workspace are displayed If you selected Intra H bonds hydrogen bonds within the selected molecule are displayed 9 2 3 Storing the Results of Measurements You can include measurements as properties in the Project Table and you can export measurements to a tab delimited or comma delimited file To create properties for measurements select Create property for selected entries before you define the measurements The measured properties are added to the selected entries in the Project Table Each distance angle or dihedral becomes a separate property and is labeled with the name Distance Angle or Dihedral and the atom numbers that define the geometric quantity For hydrogen bonds and contacts the property is the number of H bonds or contacts Each folder in the Measurements panel has a Write button which allows you to write a file containing the measurements The Write button opens a panel in which you can specify a delimiter for the file the numbering of the atoms and a file name If you specify a name or a relative path in the File text box the file is written relative to the Maestro working direc tory If you click Write To a dialog box is displayed in which you can navigate to the desired directory and select a file or enter a file name 106 Maestro 6 5 User Manual Chapter 9 Tools 9 2 4 Defining Dummy Atoms for Measurements Dummy atoms can be useful for making measurements For example you can me
65. reward term to the vdW energy Grid_philic vdW_energy oriented dipole_energy 1 where the oriented dipole energy is necessarily negative Hydrophilic regions are those within which the sum of the two terms is sufficiently negative and are displayed by contouring the hydrophilic grid at a prescribed negative isovalue typically 6 kcal mol Hydrophobic Map The quantity representing hydrophobicity is constructed by adding an oppositely signed positive electric field penalty term to the vdW term Grid_phobic vdW_energy 0 15 oriented dipole_energy 2 Hydrophobic regions thus are taken to be those for which the favorable van der Waals term is not too strongly degraded by the positive electric field penalty Qualitatively hydro phobic regions are those that lie suitably close to the surface of the receptor but for which the water dipole orienting electric field produced by the receptor is sufficiently small In short these are regions where something would like to be but water would not Hydro phobic regions are displayed by contouring the hydrophobic grid at a suitably negative isovalue typically 0 5 kcal mol The hydrophobic regions for human renin defined in this way are illustrated in the stereo pair shown in Figure 3 of Weber Halgren et al J Med Chem 1991 34 2692 2701 11 2 2 Mapping Algorithm The first step is to define a rectilinear box that contains an active site and to define grid points wi
66. specify a processor count using the syntax hostname processors An example of a host list specification is HOST florence 2 glinda The first host in the list is always the main host for the job that is the host on which the main process for the parallel or distributed job executes The LOCAL Option For some applications like MacroModel you can request temporary files to be written to the job s startup directory instead of in the scratch directory with the LOCAL option For example SCHRODINGER bmin LOCAL job name Not every application supports this option When it is supported it may be used for both local and remote jobs If you run a remote job with the LOCAL option it is important to make sure that the startup directory is accessible on the remote machine 14 6 Incorporation of Job Output When project entries are used as input for jobs the structure and property output can be incorporated into the project For Jaguar jobs the output is incorporated as a new entry automatically For other jobs you can specify how you want the results to be incorporated in the panel that is used to set up the job The three options and their effects are described below e Appending New Entries New entries are added to the project table underneath existing entries The names for the new entries have incn appended where n is a number used to ensure uniqueness of the name Replacing Existing Entries Incoming entries rep
67. the eps file extension 13 2 Creating TIFF and JPEG Image Files You can save electronic images of structures rendered in the Workspace in TIFF or JPEG format using the Save Image panel To open the Save Image panel choose Save Image from the Maestro menu TIFF files are not compressed and so are rather large However since no information is lost this file format is appropriate for producing high quality images For JPEG files Maestro uses a quality parameter of 75 by default JPEG files are compressed and subtle differences such as with colors may be noticed However these files take up much less space than TIFF files Both TIFF and JPEG files can be imported into image manipulation programs If you are running the Linux version of Maestro the Top View window does not appear in the TIFF or JPEG image even if it is visible on the screen Save Image saveimage EEE Filename amide1 jpal Image format gt TIFF 4 JPEG 75 Low lui High JPEG quality Save Save To Hide Help Figure 13 2 The Save Image panel Maestro 6 5 User Manual 159 Chapter 13 Printing and Saving Workspace Images To save an image 1 Select a format in the Image Format section 2 Enter a file name in the Filename text box or click Save To navigate to a directory and select or enter a file name 3 Click Save 160 Maestro 6 5 User Manual Chapter 14 Job Control Most computational jobs launch
68. the Entry menu or pressing DELETE The entries disappear immediately you are not prompted to confirm your choice However this function is undoable by selecting Undo entrydelete from the Edit menu of the Maestro main window 8 5 8 Moving Entries Entries in the Project Table can be moved to another location in the list Multiple entries can be moved simultaneously and entries need not be contiguous To move entries select them and then drag them to the desired new location The entries are placed after the first unselected entry that precedes this location For example if you select entries 2 4 and 6 and release the mouse button on entry 3 these three entries are placed after entry 1 because entry is the first unselected entry that precedes entry 3 To move entries to the top of the table drag them above the top of the table to move entries to the end of the table drag them below the end of the table You can also move the rows that you have selected by choosing Move Rows from the Entry menu In the Move selected entries to row dialog box you can specify the starting row number or choose to move the rows to the beginning or the end of the table 8 5 9 Sorting the Entries of a Project You can sort all entries or the selected entries by property For example if you sort project entries in descending order based on their inclusion state entries included in the Work space are placed at the top of the list and excluded entries are p
69. the Show Hide project table button in the toolbar EEA When the Project Table panel is displayed choose Spreadsheet from the Import submenu of the Table menu The Import Spreadsheet panel is displayed The layout of this panel is similar to that of the Export and Import panels with file selection tools at the top and action buttons at the bottom To select a file to import data from you can navigate to it with the file selection tools or enter its name in the File text box Import Spreadsheet spreadsheetimport EEE zone1 dya11 tutorial Filter Files ct sx vt Directories PO O comp prj ligs prj test1 csw test 7 7 BO ZE TE Launch Directory Working Directory File zone1 dyall tutorial new csv Import Filter Figure 3 5 The Import Spreadsheet panel 28 Maestro 6 5 User Manual Chapter 3 Importing and Exporting Structures and Data E xi File zonet dyall tutorial new csv File Key Match to property in Project Table Hami de Hami dine Hamine Hmetab 7 E 12 D Delimiter Comma OK Cancel Figure 3 6 The Choose Import Key dialog box When you have selected the file click Import The Choose Import Key dialog box is displayed In this dialog box you determine how the rows of the spreadsheet are mapped to the entries in the Project Table and select the delimiter The File key column lists the properties in th
70. the Workspace to the current selection 1 Choose Add from the Select menu 2 Select Included State from the Properties list 3 Select Included or fixed in the conditions section 4 Click Add then click OK 8 5 Operating on Selected Entries The Entry menu provides tools to perform various operations on the selected table entries These operations are discussed in the following sections 8 5 1 Including Excluding and Fixing Entries In addition to using mouse operations you can include and exclude entries in the Work space by selecting the entries and choosing Include Include Only or Exclude from the Entry menu The last two of these menu items are mapped to the shortcut keys ALT N and ALT X You can also include and exclude entries by property value from a plot in the Plot XY panel See Section 10 2 5 on page 117 for more information If you want to keep some entries in the Workspace while including and excluding other entries such as a receptor and a set of ligands you can select the entries you want to keep in the Workspace and choose Fix from the Entry menu or press ALT F These entries remain in the Workspace until you explicitly exclude them 8 5 2 Limiting the Number of Entries Displayed In large projects you may want to limit the number of entries displayed in the Project Table To do this select the entries then choose Show Only from the Entry menu Likewise you can hide the selected entries by choosing Hide from
71. the terminal session from which you launched the job For command line jobs this means that the UNIX command prompt is returned immediately without waiting for the job to finish This behavior is not always desirable especially if you want to run the job in a script in which some subsequent action can be taken only after the job finishes The command line option WAIT can be used to prevent the command prompt from returning until after the job finishes For example SCHRODINGER bmin WAIT job name Even with this option however the calculation is still placed in the background so pressing CTRL C or CTRL Z does not affect it If you submit a job to a batch queue however the command prompt is returned immediately regardless of the presence of the WAIT option because this option applies to the running of the program not the submis sion of the job to the batch queue The HOST Option Jobs can be submitted to a remote host using the HOST option to specify the remote host name For example SCHRODINGER bmin HOST hostname jobname For programs that can run a single job in parallel or distribute several jobs over a number of processors the HOST option can be used to specify the list of hosts to be used The host list is a list of host entry names separated by spaces The list must be enclosed in quotes if there is more than one host specified Maestro 6 5 User Manual 175 Chapter 14 Job Control Each host entry name may also
72. to build structures Building from fragments ensures the correct geometry within each fragment and thereby reduces the work needed to minimize the structure The following fragment libraries are available with Maestro Organic e L carbohydrate pyranose Rings Metal centers N heterocycles Metal ligands e O heterocycles Amino acids S heterocycles Nonstandard amino acids Mixed heterocycles Protein capping groups 32 Maestro 6 5 User Manual Chapter 4 Building Structures Carbohydrate furanose Deoxyribonucleic acids Carbohydrate pyranose Ribonucleic acids L carbohydrate furanose These libraries are described briefly below Organic This library contains the common organic functional groups a selection of simple ring structures some common ions such as hydroxide sulfate nitrate ammonium and a hydrogen molecule Rings This library contains some more complex ring structures than those in the organic fragments library including some fused ring structures a basic steroid struc ture porphyrin and phthalocyanine buckminsterfullerene and dodecaborane Heterocycles The four heterocycle fragment libraries provide a range of ring struc tures that contain nitrogen oxygen and sulfur atoms Furanose and pyranose structures Sugars can assume cyclized forms that include either five or six members The five membered ring form is called the fura nose form and the six membered version is called the pyra
73. where n is a number starting from 1 For more information on incorporating job output into the Project Table see section Section 14 6 on page 176 8 2 4 Merging Entries From Another Project You can merge the entries from a specified project into the current project There is no facility for merging a subset of entries When the merge is performed the entries are incorporated at the end of the Project Table list in the current project To copy the entries from a source project into the currently open project choose Merge from the Project menu In the Merge From Project project selector navigate to the desired source project If you want to include user created files associated with the merge source project select Include user created files If none of the incoming entries has a name identical to an entry in the current project the entry names remain intact If there are duplicate entry names in the projects to be merged the Entry Name Resolution panel is displayed and you must choose a resolution scheme in the Retain Entry Names In section Current Incoming or User Specified If you select Current the names in the current project are kept and the conflicting incoming entries are renamed Likewise if you select Incoming the incoming entries retain their names and Maestro 6 5 User Manual 79 Chapter 8 Projects the conflicting entries in the current project are renamed If you want to choose which entries to rename select User
74. work done to a particular project during a Maestro session you can revert to the opening state of a project which is saved by Maestro Like reverting to a snapshot reverting to the opening state of a project discards all work performed on that project since it was last opened in the current Maestro session To scrap the project in its present state and begin again choose Revert to Opening State from the Project menu Since the reversion is not undoable you will be prompted to confirm your choice Maestro 6 5 User Manual 101 Chapter 8 Projects 102 Maestro 6 5 User Manual Chapter 9 Tools Maestro is equipped with tools for investigating and changing the properties of structures in the Workspace While some of these tools such as plotting Chapter 10 are discussed elsewhere most of the tools are discussed here 9 1 Displaying Markers Maestro uses markers to mark atom selections in the Workspace These markers provide visual confirmation that atoms have been successfully selected or that an analysis task or operation has been performed For most operations you can choose whether or not to display markers When you are no longer using a property represented by a set of markers you can hide the markers so that the Workspace does not become cluttered The atom sets remain defined so that you can redisplay the markers later Most panels display markers by default and undisplay their associated markers when you close the panel
75. 1 1 411700 AL e ee 2 0 00000 0 00000 CHEX n i 6 0 0 1 nm 3 3 1 821477 1 772701 0 253300 LUNA 2 0 00000 0 00000 CHEX cl 6 0 0 1 nm There must be the same number of data values as there are data names and the fields within the data items must appear in the same order as the data names are listed In the above example for instance the first field in the first line of data 1 is the index number The second number 3 is the MacroModel atom type indicated by the data name i m mmod type Index numbers are required in an indexed block and do not count against data names The end of the data item section is indicated by a second separator A file may contain any number of structures CT blocks and each structure block may contain any number of atom and bond data items 186 Maestro 6 5 User Manual Appendix A The Maestro File Format A 3 Compressed Format Files may use a compressed format most commonly when storing information for a set of conformers In a compressed file the first CT block must be a full block containing all the information described above The name of this block is m ct This full block can be followed by any number of partial CT blocks with the name p_m_ct The partial blocks contain only information which is different from that in the last preceding full CT block For example a file of conformers will have only one copy of the bond table the m bond 36 block in the example file an
76. 115 Project Table panel 81 82 translations from superposition 108 locali 74 transparency surface 131 133 tube representation adjusting width of 64 U uncompressing MacroModel files 199 undoing individual operations 14 molecular transformations 15 using snapshots in 101 using the Undo menu option 14 user name setting for remote hosts 165 utility scripts applvhtreat isa 206 218 mmio convert 199 TIMO AMAS iter etre erre 199 TIMO AMO M M 200 MO LMMOA eerte eterno 200 PADCONVS Elias iris 200 Propfire sa ninia cana 204 DEODLUSCO quai ari 205 SOCODVOEtt ceret tret 202 SASUDSCE anida 204 V valency Violation of 37 39 40 van der Waals surfaces e 126 use for molecular surface generation 125 VDW Surface panel sss 126 viewing transform saving and restoring 15 VO Mecanica ici importing properties of W warning messages in Maestro PDB CONVERSION ssi 21 wire representation changing appearance of 64 SM OOM Gs oi ss 63 WORKSPACE acortar tds 6 210 adding to the selection 89 background color 146 154 creating entries from ss 79 image OUtput
77. 12 5 4 Opening Existing Command Scripts The Command Script Editor panel provides two options for locating existing command scripts To open a file selector in your working directory click the Open Local button To open a file selectorinthe SCHRODINGER maestro vversion data res directory click the Open Global button Using either file selector navigate to the desired directory select a command script and then click Open to load the script into the Script text area If there are any commands currently in the Script text area you are asked whether or not you want to replace them with the script you are about to open 12 5 5 Running and Stopping Scripts After you load a script into the Script window you can execute it by clicking Run Script If Log Commands is selected the script commands are added to the Command History list even if the command script doesn t perform any operations that are visible in the Work space To halt the execution of a script click Stop Script 12 5 6 Customizations You Can Perform With a Script As mentioned above some customization settings in Maestro are not persistent across sessions You can configure Maestro on startup according to your personal preferences by performing any of the desired operations described below making a script containing the resulting commands and then saving the script as maestro cmd in the preferences directory Before you create scripts to perform the following customizatio
78. 2 The Jaguar Read File file selector 3 2 Exporting Structures Using the Export panel you can write out structure files in Maestro MacroModel PDB Sybyl Mol2 and MDL SD formats and in various other formats available through the program Babel You can use the Workspace contents or selected project entries as input and you can append structures to an existing file and retain additional information when the file format allows it When exporting project entries Maestro provides options for exporting each selected entry to its own file or placing all selected entries in the same file Project data is automatically saved unless you are running in a non automatic synchroni zation mode The structures from a project are saved in a Maestro formatted file along with other data If you want to save just the structures and their associated data or if you want to save structures in other file formats you can export the structures To open the Export panel choose Export Structures from the Project menu on the main menu bar or choose Structures from the Export submenu of the Table menu in the Project Table panel When you have made all the necessary selections click Export A dialog box confirms that the files were written If a file by the specified name already exists the Exporting Over write dialog box is displayed and you must choose an action Maestro 6 5 User Manual 23 Chapter 3 Importing and Exporting Structures and Data Export
79. All Rows If three keys is not sufficient to sort the table in the way you want you can use the tablesortfields command in the Command Input Area to choose as many keys as you want See the Maestro Command Reference Manual for the command syntax 8 6 The ePlayer The ePlayer allows you to view in succession the structures associated with selected entries By carefully selecting entries to be included in the Workspace and then selecting an entry to be used as a reference you can use the ePlayer to visualize structure relation ships such as ligand receptor docking To use the ePlayer you must have a project open with at least one entry selected 92 Maestro 6 5 User Manual Chapter 8 Projects The ePlayer can be operated from the toolbar or from the ePlayer menu 8 6 1 ePlayer Modes The ePlayer has two modes Continuous mode and Step mode In Step mode you manu ally advance the ePlayer to show each new entry structure You can use the Next and Previous buttons on the toolbar or the Next and Previous items on the ePlayer menu Id M To go to the beginning or the end of the entry list use the Go to Start or Go to End toolbar buttons or ePlayer menu items 44 bl In Continuous mode the ePlayer automatically displays all selected entry structures in sequence You can play through the structures once or you can loop over the series by repeating the sequence of structures in the same direction or by reversing the direction These
80. Bar Options displayopt EEE Background 3D By Palette By Name Background color Figure 12 9 The Background folder of the Display Options panel Maestro 6 5 User Manual 145 Chapter 12 Customizing Maestro 12 3 1 Showing or Hiding Controls and Displays The following five items in the Display menu hide or show main window controls and displays ToolBar Topview Window Command Input Area StatusBar Sequence Viewer 12 3 2 Setting the Background Color The default background color of the main window is black but the color can be changed to adjust the contrast between the background and the Workspace atoms The background color can be retained for printing You can change the background color in the Background folder Choose a color in the By Palette subfolder or select a color by name in the By Name subfolder When a color is selected a sample of the color is displayed in the Background Color box 12 3 3 Specifying a Stereo Viewing Method Maestro s default stereo viewing method is Wall Eyed In this method of stereo viewing the left eye looks at the left image and the right eye looks at the right The other option is Cross Eyed viewing in which the left eye looks at the right image and the right eye looks at the left Maestro also supports hardware stereo display On both Linux and SGI platforms stereo in a window is supported and full screen stereo is supported on SGI platforms For det
81. Entries Using the Plot Panel esee 88 8 44 Selection Examples imet epe enitn te 88 8 5 Operating on Selected Entries iere tetro eere rester bero eere teda 89 8 5 1 Including Excluding and Fixing Entries ii 89 8 5 2 Limiting the Number of Entries Displayed sess 89 8 5 3 Rename Entes 2 be UE RE EUCH CREER M Pe subo ando 89 8 5 4 Duplicado Entes soplan cda 90 8 5 5 Merging Multiple Bates 02S 8 rende eec aah han aes 90 8 5 0 Splitting Entries by Molecule ER erre erre tet 90 8 3 7 Deleting Bniries sarete ore FE CT reae er aria 91 8 3 8 Moying EMOS aiii 91 8 5 9 Sorting the Entres of a Project encre Rie 91 8 6 There iaa 92 8 6 1 ePlayer MOSS ticos air 93 8 6 2 ePlayer ODUOILD 2 icit rete certo ree b nao Quee in epe eo Pepe ERE 93 Maestro 6 5 User Manual v Contents 5 7 Entry PEFODerties cierre tite Ree er ERIS iis 95 8 7 T Creatine New Properties ceca th rette rechte tee ere eek eret ebd 95 8 7 2 Changing Property Values i eerte eerte tor ve Vene EE 97 8 7 3 Renaming and Deleting Properties eese 99 8 7 4 Displaying Selected Properties iii 100 8 7 5 Moving and Resizing Property Columns eee 100 8 7 6 Exporting and Importing Data 101 8 8 Undoing Project Operations 101 AA aaa 103 9 1 Displaying Markers cion aaa 103 9 2 Making Measurements in the Workspace
82. Maestro 6 5 User Manual Copyright O 2004 Schr dinger LLC All rights reserved Schr dinger FirstDiscovery Glide Impact Jaguar Liaison LigPrep Maestro Prime QikProp and QSite are trademarks of Schr dinger LLC MacroModel is a registered trademark of Schr dinger LLC To the maximum extent permitted by applicable law this publication is provided as is without warranty of any kind This publication may contain trademarks of other companies Revision A June 2004 Contents Chapter 1 Document OvervieW mcommmsmmsss 1 Chapter 2 Maestro Overview s sccseccsccsscccsesssesssossonecsscsvossesssecsoenessoassoarsoessonesesese 3 21 Starting Maestro ici a sais 3 2 2 General Interface Design noni chal ies honra nali lose sia ci TRAE DER diia 4 212 Maestro Windows ciale 5 2 2 2 Mouse FUNGHODS iii 5 2 3 The Maestro Main Window isso C Recte rer pee ore errans 6 2 3 1 The Toolbar ete lea rat 7 2 3 2 Shortcut Keys loi iii 10 2A Maestro is BE 11 Ded Maestro PROC Em 11 2 6 Job Launching and Incorporation once 12 2 7 Undoing Workspace Operations 2 ia 14 2 7 1 Undoing Operations on the Structures 14 2 1 2 Undoing Operations on the View iii 15 2 8 Ending a Maestro SessIOD eie eere nee ao 15 Chapter 3 Importing and Exporting Structures and Data 17 3 1 Importe SUUCUITSS eee irr instead 17 3 1 1 Selecting Elles
83. Maestro without specifying a project to open a scratch project is created You can work with a scratch project and perform nearly all the tasks that you can perform with a named project If you want to start a new project and save its data you can create a new named project by choosing New from the Project menu The main difference between a new project and a scratch project is that the new project has a name and is automatically saved When you choose New a project selector panel is displayed This panel enables you to choose the location of the new project create a directory and type in the project name To open an existing project choose Open from the Project menu or click the Open a project toolbar button E Maestro 6 5 User Manual 75 Chapter 8 Projects A project selector panel is displayed that enables you to select a project to open The project selector panels are described in more detail in Section 8 1 4 on page 77 You can only have one project open at any time 8 1 2 Saving and Closing Projects The data in a project is normally saved automatically when you make changes to the project Changes to entries that are made in the Project Table are saved automatically The saving of changes to entries that are displayed in the Workspace depends on the prefer ences you set in the Preferences panel By default these changes are saved automatically Because the data in a named project is automatically saved you do not need to expl
84. Manual Chapter 4 Building Structures Build build PARS rio ede RR px Atom Residue Properties Properties Y I Define grow bond Mutate Il I 7 Pick Atoms Fragments Amino acids ra ALA ARG ARN ARG H ASH ASP ASN ASP cys GLH GLU H GLN GLU GLY HIE HIP HIS ILE LEU LYN LYS H LYS Grow Direction forward N to C Joining Geometry trans Secondary Structure extended Figure 4 2 The Fragments folder of the Build panel showing the Mutate option If you want to join these structures to form a single molecule you can use the tools in the Connect Fuse panel See Section 4 6 on page 40 for details You can build a single structure from multiple fragments in Place mode Once you have placed the first fragment you can join a second fragment to it by selecting the fragment from the fragments list and clicking in the Workspace on the atom that you want the new fragment to replace If you click on a terminal atom the fragment replaces the terminal atom If you click on a non terminal atom that atom and its attached hydrogen atoms are replaced by the new fragment For example clicking on a secondary amine nitrogen with a methyl fragment gives a disubstituted methyl center and clicking on a disubstituted methyl carbon with an amine fragment produces a secondary amine center You can also mutate one residue into another in a prot
85. O through 199 When adding your own types you should begin with the number 200 Negative atom types are not accepted Inside Maestro you can change atoms in existing structures to new types including user defined types However no provision is made in the current version for the builder to obtain the geometric information it needs from the atom typ file which would require extensions to the format of this file Also the original atom types remain hard wired in Maestro Therefore you should not attempt to redefine types which we supply Instead add new types The atom typ file itself contains comments describing its format and usage See the MacroModel Reference Manual for a description of the atom typ file and how to add atom types The atom types and their equivalents in other force fields are listed in Table B 1 and Table B 2 These atom types are defined in the atom typ file Note that 00 atoms are stored as type O in the atom connection table and that all current force fields require explicit hydrogens on heteroatoms Maestro 6 5 User Manual 191 Appendix B Atom Types Table B 1 Atom types and equivalents uH ON U A WwW oo 10 11 12 14 15 16 17 18 19 20 21 23 24 192 Symbol CI C2 C3 CA CB CC CD CE CF CM CP CR CO 02 03 OA OM OW OP OQ 00 N1 Description Carbon sp Carbon sp Carbon sp United atom CH sp United atom CH sp United atom CH
86. Redo Clear workspace Clear all atoms from the Workspace Enhance depth cues Optimize fogging and other depth cues based on what is in the Workspace Rotate around Y axis by 90 degrees Maestro 6 5 User Manual Tile entries Arrange entries in a rectangular grid in the Workspace Save view Save the current view of the Workspace orientation location and zoom Display only picked atoms Pick atoms to display Menu button with a pick menu Also display Add the selected atoms to the display Menu button with a list of predefined atom categories and an item to open the Atom Selection dialog box Display residues within N angstroms of currently displayed atoms Menu button with a list of values and an item to open a dialog box to set a value Draw bonds in wire Pick atoms for representation Menu button with a pick menu and an item to open the Atom Selection dialog box Draw atoms in ball and stick Pick atoms for representation Menu button with a pick menu and an item to open the Atom Selection dialog box Color all atoms by scheme Menu button with a list of schemes Label atoms Label all atoms with the selected label Menu button with a list of label types and an item to delete labels Maestro 6 5 User Manual e F Chapter 2 Maestro Overview Reset workspace Reset the rotation translation and zoom of the Workspace to the default state Restore view Restore the last saved view of the Work space
87. a displayed structure to the color green you first select the color from the Atom Coloring panel and then pick the atoms to be colored In many cases you can review the selection before applying the action Most operations are chosen by opening a panel or a folder Selecting the atoms to apply the operation to is called picking To pick an atom or a group of atoms you can click on the relevant structural elements in a Workspace structure such as atoms or residues Each panel folder or dialog box that requires a choice of atoms has a set of picking tools which vary according to the flexibility needed in the choice of atoms These tools are described in detail in Chapter 5 2 5 Maestro Projects When you use Maestro you are always working within a project A project is a collection of chemical structures and their associated data These structures and their data are orga nized into entries each of which can consist of multiple molecules and their properties The project is represented in the Project Table which displays an ordered list of entries and any associated data You can open the Project Table panel by choosing Show Table from the Project menu or by clicking the Show Hide project table button on the toolbar EH If you do not specify a project when you start Maestro Maestro creates a scratch project You can work in a scratch project but you must save it in order to use it in future sessions Entries are represented by rows in
88. a volume is selected a summary of the volume properties is displayed This information is read only and includes e Author The name of the program that created the data e Property The property represented by the grid data Data Range The range of sample point values e Origin The x y and z coordinates of the volume box origin Extent The length in angstroms of the volume box along the x y and z axes Resolution The number of grid points in each dimension When a surface is selected the lower portion of the panel contains controls for the display of the surface in two folders Drawing and Color Scheme At the bottom of the panel are buttons for creating new surfaces importing surfaces and deleting surfaces The controls and buttons are described in the next few sections 11 4 1 Changing the Appearance of the Surface You can adjust various characteristics of the surface s appearance and control whether or not it is displayed using the controls in the Drawing folder 132 Maestro 6 5 User Manual Chapter 11 Surfaces Entry benzene_hf 01 inci i Choose Entry benzene_hf 01 inci i Choose Volumes surfaces for the chosen entry Volumes surfaces for the chosen entry benzene dft 01 plot a0020 MO benzene dft 01 020_MO orbital 0 34 0cc 1 00 orbital 0020 E 0 208134 occ 1 00 benzene dft 01 plot a0021 MO benzene dft 01 plot a0021 MO orbital 0021 E 0 208134 occ 1 00 orbital 0021 E 0
89. age Scale To Page Select Scale to Page to reduce or enlarge the image to occupy the available space on a standard page When Scale to Page is not selected the image is printed roughly the same size as it appears on screen Color Mode The Color Mode selections are Color Grey scale Black Text and Black Text amp Lines Selecting the Color Grey scale option allows you to print or save images exactly as they appear on screen If atom labels and other text appears in color they are printed in color It can be difficult to read atom labels and other text in color To force atom labels and any Maestro 6 5 User Manual 157 Chapter 13 Printing and Saving Workspace Images other text to print in black select Black Text To force text plus any lines such as markers and wire frame bonds to print in black select Black Text amp Lines If you print to a black and white printer the images are printed in grey scale instead of color Print Background This button controls the printing of the background color of the Workspace It is not selected by default because printing a background requires more ink or toner and time and the default background color of the Workspace is black Surface Smoothness Increasing the surface smoothness for an image helps to remove blocky edges on curved surfaces in your structure However there is a trade off between degree of smoothing and amount of print time required Particularly with small curve
90. ails see the Schr dinger Product Installation Guide The stereo viewing controls are in the Stereo subfolder of the 3D folder To select a stereo viewing method choose Wall Eyed Cross Eyed or Hardware from the Method option menu To view the Workspace in stereo select Display in Stereo If you are using the cross eyed or wall eyed method and the displayed stereo pairs are more than 2 5 inches from each other adjust the Size Factor and Scale Factor controls to bring the structures closer This will make stereo viewing easier With any stereo method you can adjust the eye separation and the alignment depth Adjusting the eye separation changes the amount that the stereo image appears to extend into and out of the screen the stereo depth and adjusting the alignment depth makes the stereo image appear to move into or out of the screen 146 Maestro 6 5 User Manual Chapter 12 Customizing Maestro Display Options displayopt ETE Background 3D Stereo Perspective Fog W Display in stereo Method Wall eyed Size factor 0 00 mma Separation factor 1 00 CD Eye separation stereo depth Alignment depth W Adjust clipping to preserve depth cues Enhance Depth Cues Figure 12 10 The Stereo folder of the Display Options panel 12 3 4 Enabling Perspective Maestro s Perspective feature enhances 3D graphical representation by scaling items in the Workspace in proportion to their distance to the viewing
91. ain in later Maestro sessions To save a set definition to disk click Write The Write Set Files panel is displayed In this panel navi gate to the directory in which you wish to save the set definitions and enter a name for your sets definition file The extension set is automatically appended to the file name Click Write to save the file and dismiss the panel The procedure to read an existing sets definition file is similar Click Read in the Sets panel then navigate to the desired directory and select the file in the Read Set Files panel and click Read 9 5 Assigning and Aligning Protein Structures Maestro has tools for aligning protein structures and for assigning secondary structures in proteins If you want to bring two or more proteins into a common frame of reference by structur ally aligning superimposing them you can use the Protein Structure Alignment panel which you open from the Tools menu To use this panel you must have a Prime license For information on this panel see the Prime User Manual or the online help for the panel Maestro 6 5 User Manual 111 Chapter 9 Tools The Assign Secondary Structure command on the Tools menu provides a way of assigning secondary structure to a protein The assignment occurs in two stages First all inter back bone hydrogen bonds are identified Second a search is made for hydrogen bonding patterns representing helices and strands The assignment is used for the display of r
92. an also select multiple data points and their corresponding entries by drag ging All the data points in the bounding box have their entries included in the Workspace In amp 10 3 Editing Plots and Plot Settings The Plot Settings panel is used to select plots edit plot properties edit X and Y axes and add edit and delete data series To open the Plot Settings panel choose Plot Settings from the Settings menu of the Plot XY panel or press ALT P You can select multiple plots in the list of plots but you can only change the settings when you have a single plot selected Maestro 6 5 User Manual 117 Chapter 10 Plotting 10 3 1 Modifying Plot Attributes The tools in the Plot folder allow you to modify plot attributes other than the plot line Displaying and Undisplaying a Plot To display a plot select Plot displayed To hide a plot deselect Plot displayed Modifying a Plot Caption When you create a new plot a caption is displayed under neath the plot in the Plot XY panel by default The default caption contains the assigned caption text as well as the plot name To modify the caption content type the new caption in the Caption text box To change the contents or placement of the caption or to undisplay the caption select the appropriate options Displaying Selection and Inclusion Markers By default points corresponding to selected and included entries are not marked To display the markers select Display selected en
93. and click Delete 9 4 2 Selecting Atoms for a Set To define the atoms that make up a set select the set from the set list then use the tools in the Atoms For Set section to select the atoms You can pick the atoms using the picking tools enter an ASL expression in the ASL text box or click Select to select atoms using Maestro 6 5 User Manual 109 Chapter 9 Tools ijmix Name Set1 Atoms for set ASL atom num 22 Clear a Select W Pick Atoms ME Show markers W Apply marker offset New Delete Read Write Boolean Hide Help Figure 9 4 The Sets panel the Atom Selection dialog box The Atom Selection dialog box has a Create Set button which you can use to create a set at any time not just from the Sets panel If you select Show Markers the atoms in the set are marked with green markers If the markers obscure part of the structure that you want to see you can move them slightly by selecting Apply Marker Offset This button is selected by default For more information on ASL see the Maestro Command Reference Manual Chapter 3 For more information on the Atom Selection dialog box see Section 5 2 on page 54 9 4 3 Creating Sets With Boolean Operators Boolean operators may be applied to one or two existing sets to create new sets This option is useful if you wish to create a new set that can be defined in terms of existing sets To create a new set using b
94. ange the name of the displayed surface or volume edit the name in the Name text field 136 Maestro 6 5 User Manual Chapter 12 Customizing Maestro Many aspects of the Maestro interface can be customized Some of the changes can be saved explicitly using the Preferences Macros and Command Aliases panels so that they are preserved in subsequent Maestro sessions The changes are stored in the HOME schrodinger maestrovv directory where vv is the two digit Maestro version number 60 for this release This directory is referred to hereafter as the preferences directory Other changes can be preserved only by creating a startup script that issues the Maestro commands necessary to generate the desired changes when Maestro is launched You can create startup scripts even if you are not familiar with the Maestro Command Language because most of the commands that you may want to include in a startup script can be extracted from the Command History log in the Command Script Editor panel 12 1 Changing and Saving Panel Layout Although effort has been made to optimize the default window positions and dimensions you may want to change them Resizing and repositioning windows is done in the normal way by dragging a corner a side or the title bar of the panel Here windows means panels dialog boxes and the main window You can also hide all panels except the main window display all panels and arrange the panels in a cascade from upp
95. annot be used with b The m can be omitted if this option is at the end of the option list p project Load the specified Maestro project s number Specify the first structure to load when a Maestro file is specified for loading t number Specify the total number of structures to load when a Maestro file is specified for loading v Display the Maestro version number but do not start Maestro I Display extra information about X visual settings when Maestro starts SGL Use the Schr dinger supplied OpenGL library The default is to use the system OpenGL library The directory from which Maestro was started becomes Maestro s current working direc tory and all data files are written to and read from this directory unless otherwise speci fied You can change directories by entering the following command either at the shell prompt before you start Maestro or in the command input area of the Maestro main window cd directory_name where directory_name can be either a full path or a relative path 2 2 General Interface Design The Maestro interface design makes use of most of the common features of interface design but it has some characteristics that are unique The general operation of the Maestro interface is described in this section Other interface features that are specific to Maestro are described in the relevant sections or chapters 4 Maestro 6 5 User Manual Chapter 2 Maestro Overview 2 2 1 Maestro Windows
96. ap panel choose Sitemap from the Surfaces submenu of the Display menu 11 2 1 Background Given a receptor structure SiteMap partitions the accessible space in the active site into three types of regions 1 Hydrophobic regions that are favorable for occupancy by hydrophobic ligand groups 2 Hydrophilic regions that are favorable for occupancy by hydrophilic ligand groups 3 Neither hydrophobic nor hydrophilic regions that are of mixed character or that are far enough from the receptor surface to be similar to bulk water where to a first approximation any group could reside with little effect on the binding affinity Hydrophobic and hydrophilic regions are marked by surface contours that enclose the region The neither regions in contrast are implicit these are simply regions that are accessible to the ligand but are not marked as being either hydrophobic or hydrophilic By revealing targets of opportunity e g hydrophobic regions that have room to accommodate a larger hydrophobic group active site maps can aid in the design of new ligands Alternatively by showing the degree to which poses produced by a program like Glide display or violate proper complementarity to the receptor site site maps can aid in the evaluation of docking hits The neither regions are also important because they are regions in which the physical properties of the ligand can be changed for example to make the ligand more or less solu
97. as the movement of one molecule with respect to another If you want to perform a translation you need only select the atoms for transformation If you want to perform a rotation a rotation center is required Maestro provides a default but if this is not satisfactory you must choose a rotation center The controls for local transformations are available from the Advanced Transformations panel which you open by choosing Global Local from the Local transformation button menu in the toolbar E 1 The subset can in fact include all atoms in the Workspace so that the rotation or translation actually changes the coordinates of the entire contents of the workspace 72 Maestro 6 5 User Manual Chapter 7 Manipulating Structures Advanced Transformations advtransforma BRITES Atoms For Transformation Clear All Select W Pick Molecules LI Show markers A Center For Transformation ASL 72 al Select y Pick Molecules LI Show markers Rotation Translation Scope lt Global 4 Local Hide Help Figure 7 1 The Advanced Transformations panel The picking tools for defining atom sets are also available directly from this button menu The selections you make in the Advanced Transformations panel persist even when you alter the structures in the Workspace To clear them click Clear Local transformations are performed with the same combination of keys and mouse move ments as gl
98. asure the distance between the centroids of two ring systems by placing dummy atoms at the centroids You can place dummy atoms in two ways 1 Use the Centroid panel to define a centroid atom A dummy atom is placed at the mean position of the picked atoms 2 Use Draw mode in the Build panel to place an atom in the Workspace then retype it with the appropriate MacroModel atom type Several kinds of dummy atoms are defined in the Atom Type Macromodel list in the Atom Properties folder of the Build panel If you attach the dummy atom to your structure you can adjust its position using the Adjust panel 9 3 Superimposing Structures Ifyou want to determine the similarity of structures such as a set of conformers or a family of ligands docked by Glide you can display the structures in the Workspace and then use the tools in the Superposition panel to evaluate the differences in the atom positions Each structure must be in a separate project entry The superposition scheme works by aligning the first selected atom in each structure then attempting to align the second selected atom and so on After superimposing atoms the results of the operation are displayed in the RMSD text box near the bottom of the panel The results include the molecule numbers the RMS deviation of the atoms from those of the first structure and the maximum difference between superimposed atom positions To open the Superposition panel choose Superposition from t
99. ation 5 mae File Name Automatic Number If you select File Name Automatic Number you must specify a filename The files are given the same name and extension as the selected file but numbers are added in sequence to the base file name For the same example as above if you select the file structure dat the new files are named structure 1 dat structure 2 dat structure 3 dat Just Entry Names If you choose Just Entry Names the file name is constructed from the entry name For the above example the new files are named combination 3 mae combination 4 mae combination 5 mae and a dialog box confirms that the files were written to the desired directory 3 3 Exporting Data to a Spreadsheet The Project Table does not have spreadsheet capabilities but you can export data to a spreadsheet file manipulate it in a spreadsheet program then re import it into Maestro Exporting data to a spreadsheet file is done from the Export Spreadsheet panel The data that you can export are the properties in the Project Table To export data you must first open Project Table panel which you can do by choosing Show Table from the Project menu in the main window or clicking the Show Hide project table button in the toolbar EH When the Project Table panel is displayed choose Spreadsheet from the Export submenu of the Table menu The Export Spreadsheet panel is displayed The layout of this panel is similar to that of the Export and Import pane
100. ation panel choose Molecular Representation from the Display menu 6 2 1 Changing the Representation of Atoms In the Atoms folder you can choose between None CPK and Ball amp Stick for the represen tation of atoms The None option means that only the bonds are depicted The bond repre sentation is set in the Bonds folder To change the representation of the atoms use the picking tools or the Select button in the Apply current representation to atoms section to select atoms to apply the representation or click All to apply the representation to all atoms You can mix representations within a single molecule by picking Maestro 6 5 User Manual 61 Chapter 6 Displaying Structures Molecular Representation rep EEE Settings Atoms Bonds Ribbons Representation 4 None Q CPK x Ball amp Stick Apply current representation to atoms W Pick Atoms All Select Figure 6 3 The Atoms folder of the Molecular Representation panel The Ball amp Stick option sets a representation for both atoms and bonds When you pick an individual atom in this representation half of each bond attached to the picked atom is displayed in stick form You can apply a molecular representation using the Draw atoms in CPK representation and Draw atoms in Ball amp Stick representation buttons on the toolbar Click either button to pick the objects to apply the representation to Double click either button to apply the
101. atment panel which you open from the Edit menu To select a hydrogen treatment choose an option from the Treatment option menu A description of the treatment is displayed in the Description text box including the force fields for which the treatment is valid This information is also given in Table 4 1 Hydrogen Treatment htreat Eix Treatments All atom with No Lp a Description An all atom treatment which does not include lone pairs This treatment is suitable for the MM3 AMBERS4 MMFF MMFFs OPLSAA and OPLS2003 force Modify hydrogen treatment W Pick Atoms Select Figure 4 7 The Hydrogen Treatment panel Maestro 6 5 User Manual 43 Chapter 4 Building Structures Table 4 1 Appropriate hydrogen treatments for Maestro supported force fields lt io x P n en a E E E Z5 n Hydrogen Treatment E S E zz og Method z lt lt gt Jo o All atom with No Lp X X X X X X All atom with Osp3 Lp X Csp3 United atom with X S Lp Csp3 United atom with X No Lp All atom with S Lp X Csp2 sp3 United atom X with No Lp a Inaunited atom representation hydrogen atoms are incorporated into the dimensions of the heavy atom to which they are attached That is they are implicit You can apply the selected treatment to the entire structure or to selected parts of the struc ture To apply the treatment to the entire structure click All in the Modify Hydrogen Treat ment section T
102. atures to build import and manipulate molecular structures No prior knowledge of Maestro is assumed If you cannot find the information you are looking for in this document see the Maestro online help For help with preparing and starting computations see the user manual for the related product For a list of features that are new in this version of Maestro see the Maestro Release Notes In addition to the normal use of italics for names of documents the font conventions that are used in this manual are summarized in Table 1 1 In descriptions of command syntax the usual UNIX conventions are used braces enclose a choice of required items square brackets enclose optional items and the pipe symbol separates items in a list from which one item must be chosen Angle brackets lt gt are used to denote user replacement text in expressions whose components are not separated by spaces Lines of command syntax that wrap should be interpreted as a single command In this document to type a command means to type the required text in the specified loca tion and to enter a command means to type the required text and then press the ENTER key Table 1 1 Font conventions Font Example Use Sans serif Project Table Names of GUI features such as panels menus menu items buttons labels Monospace SSCHRODINGER maestro File names directory names commands and environment variables Italics filename Text that the user
103. bar Those that perform simple tasks like clearing the Workspace Those that show and hide panels or open dialog boxes Those that display a menu when you click and hold The third type of button is called a menu button and has a triangle in the lower right corner The menu is called a button menu There are two kinds of items on button menus and both kinds can be on the same menu Actions which perform an action immediately States which you set before an action is performed When you select a state it is stored and marked with a red diamond on the menu Most states on button menus are pick states see Section 5 2 on page 54 which means you must pick an atom in the Workspace before the action is performed If you click a menu button that has pick states the button is indented to indicate that picking with the selected pick state is in effect If you double click a menu button that has pick states the action is applied to all atoms Some other menu buttons support double clicking to apply an action this support is explicitly mentioned in the button description Maestro 6 5 User Manual 7 Chapter 2 Maestro Overview You can show or hide the toolbar using the collapse button at the top or by selecting Toolbar from the Display menu You can hide it or move it to the right or left side of the Workspace by right clicking in the toolbar and selecting the appropriate option The buttons are described below Open a project Open t
104. bar fe 74 Maestro 6 5 User Manual Chapter 8 Projects When you use Maestro you are always working within a project Projects are made up of entries which can include multiple structures as well as properties of those structures Project entries and their properties are displayed in the Project Table You can perform a variety of operations on entries through the Project Table By default the Project Table panel is opened automatically when you open a project You can change this behavior in the Preferences panel To open the Project Table panel choose Show Table from the Project menu or click the Show Hide Project Table button in the toolbar EEA The project data is stored in a directory whose basename has the extension prj This directory is created in Maestro s current working directory If you have not explicitly opened an existing project or created a new project a scratch project is created in the directory specified by the environment variable TEMP_PROJECT The default location is SHOME schrodinger tmp This chapter discusses in some detail how to use the Maestro Project Facility 8 1 Project Operations The Project menu of the main window enables you to perform operations on the project level To perform operations on entries in the current project use the menus in the Project Table panel This section describes the operations that you can perform on projects 8 1 1 Creating and Opening Projects When you start
105. ble with minimal expected effect on the binding affinity The active site mapping procedure operates in a manner analogous to Goodford s GRID algorithm P Goodford J Med Chem 1985 28 849 In SiteMap hydrophilic and hydrophobic regions are defined in a way that considers both spatial proximity to the receptor and suitability for occupancy by solvent water A putative van der Waals energy and the magnitude and direction of the electric field calculated using a distance depen dent dielectric formulation are computed for a probe centered at each grid point by considering interactions with all atoms of the receptor site within a defined cutoff distance In contrast to techniques that color code the receptor surface to represent hydrophilicity or hydrophobicity site maps depend on more than the character of the nearest receptor atom Moreover site maps explicitly show the shape and extent of hydrophilic and hydrophobic regions something a receptor surface display cannot do The site maps behave rather like Maestro 6 5 User Manual 127 Chapter 11 Surfaces an extraradius surface in that the atoms of a stick figure representation of the ligand can approach but should not penetrate the site map surface except in hydrogen bonding regions where internuclear distances are expected to be smaller than normal contact van der Waals distances Hydrophilic Map SiteMap constructs a measure of hydrophilicity by adding an elec tric field
106. ce you have defined the criteria for selecting entries the current entry selection can be stored as a named filter To create a filter click Create Filter The New Filter dialog box opens in which you can provide a name for the filter The newly created filter appears in the Filters folder of the Entry Selection dialog box and on the Filter submenu of the Select menu 8 4 3 Selecting Entries Using the Plot Panel The Plot panel provides a means of graphically selecting entries and including them in the Workspace By plotting a property value against the entry name for example you can view the properties and select the entries on the plot that you are interested in See Section 10 2 4 on page 117 for more information 8 4 4 Selection Examples There are generally multiple ways to perform each selection operation from an option on the Select menu using the Entry Selection dialog box using the mouse and using ESL A few examples of the use of the Entry Selection dialog box are provided here To select a range of entries with the same base name 1 Choose Only from the Select menu 2 Select Entry name from the Properties list 3 Select Matches in the conditions section and enter entry name in the text box where entry name is the base name of the entries you want to select and is a wildcard character that represents any string 4 Click Add then click OK 88 Maestro 6 5 User Manual Chapter 8 Projects To add entries from
107. cj is added to the entry name 3 1 5 Reading Jaguar Input Files Jaguar maintains its own input files which include calculation options in addition to the molecular geometry and may also include molecular orbitals In addition Jaguar can read a wide variety of input file types from other quantum chemistry codes using the program Babel Therefore Jaguar has a separate file reading mechanism When you read input files through Jaguar the structures are displayed in the Workspace and Maestro formatted files are created To read input files through Jaguar choose Jaguar from the Applications menu then click Read in the Jaguar panel The Read File file selector is displayed Navigate to the direc tory containing the file and select the file Choose the file type from the File Format option menu and change the Read as setting if necessary Click OK to read the file For more information see the Jaguar User Manual The full list of file types read by Babel is included in that document 22 Maestro 6 5 User Manual Chapter 3 Importing and Exporting Structures and Data Filter zone1 juliem jaguartest in Directories aS 01 plot in 3rdbenzeneretest prj benzene dft in methylamine pka benzene hf 01 in benzene hf in benzene mp2 01 in benzene mp2 in methylamine in SS res P File Format Jaguar input m Read as Geometry and settings Selection zone1 juliem jaguartest benzene dft 01 ini Figure 3
108. ck Entries WE Show markers Surface context 4 Entry Molecule lt Selected atoms Probe radius 1 40 Create Surface Hide Help Figure 11 2 The Extended Radius Surface panel To open the Extended Radius Surface panel choose Extended Radius from the Surfaces submenu of the Display menu Instructions for using the settings in the Extended Radius Surface panel are described in Section 11 1 1 on page 123 11 1 4 van der Waals Surfaces The VDW Surface panel is used to generate a van der Waals surface This surface is iden tical to the CPK molecular representation with the percentage set to 100 To open the VDW Surface panel choose van der Waals from the Surfaces submenu of the Display menu Instructions for using the settings in the VDW Surface panel are described in Section 11 1 1 on page 123 126 VDW Surface surfacevdw BEI WOW Surface Atoms for surface display as Ee Select W Pick Entries WE Show markers Surface context Entry lt Molecule lt Selected atoms Create Surface Hide Help Figure 11 3 The VDW Surface panel Maestro 6 5 User Manual Chapter 11 Surfaces 11 2 Sitemaps SiteMap is a 3D graphics tool that is designed to help you to visualize the preferred loca tions of ligand atoms in a receptor site Using the Sitemap panel you can generate a surface that displays hydrophobic and hydrophilic regions within the active site of a protein To open the Sitem
109. ck Intersect to restrict the current ASL expression to be applied only to protein backbone atoms To select all side chains within 5 0 of a ligand in the active site of a ligand receptor complex 1 In the Entry folder select the entry name for the ligand from the list of entries 2 Click Add to make this entry name the current ASL expression 3 Click Proximity to open the Proximity dialog box 4 Enter 5 0 in the text box click Residues in the Fill section select Exclude Source then click OK 5 In the Residue folder select the Backbone Side Chain property 6 Select the Sidechain option 7 Click Intersect to restrict the current ASL expression to include only atoms in the protein side chain To select a range of residues but exclude proline residues 58 1 NY OQ tA A W N In the Residue folder select Sequence from the property list Select the appropriate chain from the list of chains in the top scrolling list Select a range of residues in that chain from the lower scrolling list Click Add to make this residue range the current ASL expression Select the Residue Type property Select PRO from the list of residue types Click Subtract to exclude proline residues from the current ASL expression Maestro 6 5 User Manual Chapter 6 Displaying Structures Maestro provides a wide selection of options for displaying structures For example you can change the color of some or all of the atoms
110. ct 4s Filter zonet dyall pr Directories fzoneit dyall fzonet dyall zone1 dyall GRASI zone1 dyall Tutoi zone1 dyall basi zone1 dyall built zone1 dyall docs fzonet dyall fmin Items Srings prj A metal_ligands prj organic prj rings prj surf prj test prj EIA Launch Directory 2 Working Directory Project zone1 dyall new prjl Figure 8 1 The Save Project as project selector Maestro 6 5 User Manual Save Filter Cancel Make Dir TL Chapter 8 Projects the current selection If you are creating a new project saving a scratch project or copying a project enter the project name at the end of the text You do not need to add the prj extension which Maestro supplies if it is absent Making New Directories Some of the project selectors have been equipped with the ability to make new directories The Make Dir button in these project selectors opens the Make Directory directory selector To create a directory navigate to the desired location and type the new directory name at the end of the path information in the Project text box You can only create one new directory level at a time To create multiple directory levels you must use this procedure for each level you want to create 8 1 5 Annotating a Project Because projects are frequently modified it may be helpful to annotate your project Maestro provides a project annotation feature that al
111. ct can be one of atoms bonds chains residues molecules or entries The number of objects available in the menu depends on the operation For instance when you define a dihedral angle you can pick either four atoms or three bonds The Pick menu for this operation therefore only contains the items Atoms and Bonds Atoms for set ASL atom num 22 Clear All Select W Pick Atoms M Show markers Label atoms W Pick Atoms Al Select Define atoms for dihedral adjustment W Pick Atoms WE Show markers Figure 5 1 Examples of picking tools Top from the Sets panel Center from the Atom Labels panel Bottom from the Adjust panel Maestro 6 5 User Manual 53 Chapter 5 Selecting Atoms mxi Atoms for set ASL atom num 22 Clear AI Select W Pick Atoms W Show markers Residues Chains Molecules Entries Hide Help Read write Boolean Figure 5 2 The Sets panel showing the pick menu The object you choose determines the atoms that are selected when you click on an atom in the Workspace A click on a single atom in the Workspace can represent the selection of just that atom or the selection of the molecule residue chain or entry of which it is a member Successive clicks add atoms to the selection If the object is Bonds the two atoms that define the bond are selected when you click on the bond When an objec
112. d it will be stored in the full CT Subsequent partial CT blocks will read bond information from the preceding full CT block A 4 Data Item Names The names of data items in a Maestro format file follow a convention which allows the type of the data item and the owner of the data to be identified Names have the form t o d where t is the type descriptor o is the owner and d is the actual data name For instance the first data name in them bond 36 blockis i m mmod type The first character of the name represents the data type The acceptable types are 1 integer s string value r real number b Boolean value Owner values indicate the application from which the data item most likely originated Including this field in the data name allows multiple applications to store identically titled quantities For instance two applications could store data fields named energy Currently basic geometrical and connectivity information which is shared by most Schr dinger applications have m for Maestro owner fields Data introduced by Macro Model have mmod owner fields data introduced by QikProp have qp owner fields Inthe i m mmod type example i indicates the value in the corresponding data field is an integer The letter m in the owner field means that the data originated from Maestro and mmod_type is an abbreviation for MacroModel atom type which is what the data field represents A 5 E
113. d on each axis from the X Property and Y Property lists The default plot type is a line plot If you want to generate a plot of frequency of occur rence of a range of values against the midpoint of the value range select Frequency Plot An extra section is displayed In this section you can choose to display the frequency on the x axis or the y axis You can only choose one property for a frequency plot The prop erty that you select is divided evenly into ranges based on the maximum and minimum values of the property and the number of buckets you enter in the Buckets text box You can modify the appearance of the data point markers and the plot line using the option menus in the Style of Drawing section Color Marker Line Style and Line Width When you have finished characterizing the plot click New The Plot XY panel is updated with the new plot Maestro 6 5 User Manual 113 Chapter 10 Plotting mor name plot 4 Series name Series X axis X X property Entry Name Selected In surf Y axis Y Y property Entry Name Selected In Surf Frequency plot Qvientatian Buckots Drawing Style Color black ca Line style Solid Aa Marker Filled square Line width 1 New Cancel Figure 10 1 The New Plot dialog box 10 2 Viewing and Manipulating Plots The Plot XY panel is used to add edit view and delete XY plots To open the Plot XY panel choo
114. d results in the following selections If the most recent version is for an older architecture e g MIPS 3 when MIPS 4 is also available the most recent version for the newer architecture is selected If the version found in the directory specified by the schrodinger settings for localhost is more recent than the version found for the host entry the localhost version is selected If the version found in the directory specified by SCHRODINGER is older than the version found in any of the directories specified in the schrodinger hosts file the SSCHRODINGER version is selected When a job is started on a remote host the execution host the startup script for the program is run on the local host the submission host and is selected from the versions available on the local host as described above On the execution host a list is compiled sorted as described above combining lists from the following sources in the order given 1 Software in the same directory as the startup script on the submission host 2 Software in the directory specified by the schrodinger settings in the localhost entry and the entry for the host in schrodinger hosts on the sub mission host 3 Software in the directory specified by SCHRODINGER on the execution host 14 2 Monitoring Jobs When a computational job is started Maestro immediately goes into monitoring mode The Monitor panel opens and the log file for the job is displayed in the t
115. d surfaces the minute improvement in image clarity obtained from increasing the smoothness factor may not justify the increased time it takes to print the image To change the surface smoothing drag the Surface Smoothness slider Title You can enter a title in the Title text box The title is printed in black text in the lower left corner of the page Print print EIEE File format Color mode 4 Postscript PS 4 Color grey scale gt Encapsulated PS EPS lt Black text Orientation y Black text amp lines Portrait Print background B LI J Scale to page Surface smoothness vy Landscape Title Print to lt Printer 4 File Write Print cammamtz lpr Hide Help Figure 13 1 The Print panel 158 Maestro 6 5 User Manual Chapter 13 Printing and Saving Workspace Images Print Command If the UNIX shell you use requires a different print command from the default given in the Print Command text box change the command in the text box to the required command When printing an image Maestro creates a temporary PostScript file then prints this file using the specified command If your printer requires the 1p command instead of 1pr use the c option to ensure that the temporary copy of the file to be printed is preserved until printing is complete Filename If you are saving an image to a file enter the file name in the Filename text box including either the ps or
116. d when the job finishes As the job progresses any interim structures are shown in the Workspace In addition LigPrep jobs can read structures from external files This choice of structural input has no connection with a Maestro project so the output is required to be written to an external file Jaguar Jaguar maintains its own input and output files and directory structure However 1t can use Maestro structure files project entries and structures displayed in the Workspace for geometry input and inherits default directory and file settings from Maestro Jaguar can also use multiple entries selected from the Project Table as input for jobs As for Macro Model any changes to the structure are displayed in the Workspace as the job proceeds Jaguar jobs launched from Maestro are automatically monitored and the results incorpo rated into the project as new entries Numerical data such as the total energy are included as entry properties Data for display of surfaces and vibrational data are automatically incorporated when the job input comes from the Project Table FirstDiscovery The programs comprising the FirstDiscovery suite have differing degrees of integration with the Project Facility Glide can use selected entries from the project table as input for docking but does not incorporate the results The pose files that are generated are better viewed in the Glide Pose Viewer than in the Project Table Liaison is not integrated with the p
117. dently apply fogging to atom labels using the Display Fog on Atom Labels option You can also turn fogging on or off with the Set fog display state button menu in the toolbar Q The default method for fogging employs linear fall off for the brightness of the displayed structural elements To exaggerate the fogging effect you can select either the Exponential method or Exponential Squared method When you are displaying a structure in perspec tive you should use linear fall off The points at which fogging begins and ends can be controlled with the Linear Start and Linear End sliders Adjusting Linear Start moves the boundary at which fogging starts between the front 0 0 and the back 1 0 of the displayed structure Adjusting Linear End moves the fog boundary that is behind the structure further back to a maximum of twice the depth of the displayed portion of the structure By adjusting these boundaries you can control the amount by which the structure appears to fade into the background For exponential and exponential squared fogging methods the Density slider allows you to change the contrast of the colors used in fogging Higher density makes closer portions of the structure appear brighter and more distant ones fade more quickly into the background 148 Maestro 6 5 User Manual Chapter 12 Customizing Maestro Display Options displayopt ETE Background 3D Stereo Perspective Fog Display fog On W Display fog o
118. der 144 Delete Markers folder 138 Directory folder 141 File Suffix folder 143 Font Size folder 139 Label tods catarata Mouse folder Project folder Print panel cicer trn printing command IA 139 enhancing surface smoothing for 158 PostScript and EPS files titles ien ets Workspace background color 158 Workspace image sss 157 probe radius for surfaces 124 processors setting number for a host 166 project entries see entries project selectors sees TI Project Table ninia 210 Project Table panel 12 81 projects ine uan 11 209 availability indicators for IT Mn iniciada 76 creating snapshot e 101 deleting ice cet ntes 76 incorporation of job results 176 locked tete TI o esce rn 79 OPening ie wa TO opening state reverting to 101 A IN a TO saving SCratch iene 76 scratch 11 75 properties of entries 95 101 A 95 COPYING iii calas 98 216 creating from measurements 106 creating from superposition 109 Pasting Values iene 97 plotting ita 115
119. displays a set of tools that you can use to change the property Apart from the Element property the properties are listed below with a description of the tools Before you change atom properties it may be helpful to display atom labels For atom labeling information see Section 6 3 on page 67 Atom type MacroModel A list of atom type symbols with a brief description is displayed The atom type symbols represent atoms with specific properties such as sp hybridization for a C atom with type symbol C3 or a free radical for a C atom with type symbol CR The use of atom types is provided primarily for MacroModel users though Maestro always assigns an atom type to each atom For information on atom types see Appendix B To retype an atom choose the atom type and click on the atoms in the Workspace that you want to change Build build Hemi AlX io edequ 5 adah Atom Residue Properties Properties Property Atom Type MacroModel e Fragments JE Set atom type MacroModel atom CH SP3 atom CH2 SP3 atom CH3 SP3 atom CH SP2 atom CH2 SP2 atom CH SP Carbanion Carbocation Carbon free radical Any Carbon Oxygen Double Bond Oxygen Single Bonds United Atom OH alkoxide carboxylate United atom H20 Water Oxonium ion sp2 Oxonium ion sp3 Any Oxygen Figure 4 8 The Atom Type MacroModel tools in the Atom Properties folder
120. dition to the fragments the Fragments folder of the Build panel contains controls for setting the joining geometry and where applicable secondary structure and helix geom etry The Joining Geometry option menu provides context sensitive options for attaching new fragments to the existing structure For example under the Deoxyribonucleic acid fragment type the joining geometry options are Standard Helix and User Defined If you choose to define your own joining geometry you must specify values for the torsions that define applicable secondary and tertiary structures When you select the User Defined option and click on the name of the fragment a dialog box prompting you to enter an angle value is displayed Enter a value and click OK 4 3 Building a Structure From Atoms The toolbar of the Build panel contains tools for drawing structures in the Workspace atom by atom and the Atom Properties folder and the toolbar contain tools for retyping atoms within a structure Maestro does not automatically correct geometries of structures created in Draw mode You can adjust the geometry after building the structure from the Adjust panel You should also minimize the energy of the completed structure When using Draw mode to create a molecular structure only a few elements H C N O P and S are available If you want to include different elements use these elements to draw the structure and then change the desired atoms see Section 4 4 Maes
121. dividual commands can be selected or deselected by clicking A group of commands can be selected by dragging To select all of the commands in the list click Select All To deselect all the commands in the list click Deselect All Once you have selected the desired commands copy them to the Script text box by clicking Copy Selection To Script Copying many commands may take some time To interrupt the copying process click Stop Copy This button is only active during a copy Operation The commands are copied to the location of the cursor which is placed at the end of the text after a copy operation Therefore repeated copy operations append the new command selection to the commands in the Script text area If you want to create a new script you must first delete the commands from the Script text area The commands in the Command History list remain selected after the copy operation and must be explicitly deselected You can also directly enter commands in the Script text area 152 Maestro 6 5 User Manual Chapter 12 Customizing Maestro 12 5 3 Saving a Command Script To save the command script displayed in the Script text area click Save As The Save Script File file selector is displayed Navigate to the directory into which you want to place the file type the name of the file to be created at the end of the line of text in the Selection box and click Write You must include the cmd extension when specifying the file name
122. ds for full see below m generally stands for Maestro because the data origi nated from Maestro and ct stands for CT short for Connection Table which can generally be thought of as a collection of atoms Maestro 6 5 User Manual 185 Appendix A The Maestro File Format Blocks can be nested within other blocks and if a block contains a list of data values the block may be indexed That is the number of data values contained in the block can be appended to the name Indexed blocks are identified by having names of the form name lt number of items gt For example the file shown in Section A 5 contains an indexed block of the name m_atom 18 In this block name m means that the data originated in Maestro atom means that the data values included in the block belong to atoms and 18 indicates that are 18 sets of data in the indexed block representing 18 atoms Within each block there are two sections a list of the names corresponding to the data fields included in each data item and the actual data items In the example file the first three data field names in the m_atom 18 block are i m mmod type r m x coord r m y coord The end of the first section is denoted by a separator and followed by the actual data items In the example file the first three data items are 1 3 0 547623 1 262401 0 990300 qoo X cm 2 0 00000 0 00000 CHEX E 6 0 0 1 me 2 3 0 930177 1 29670
123. dsheet file See Section 3 3 on page 26 and Section 3 4 on page 28 for information on exporting and importing properties Most of the operations you can perform on properties are available from the Property menu Others such as plotting importing and exporting are available from the Table menu 8 7 1 Creating New Properties Apart from incorporating results from a calculation and importing data from a spread sheet there are some ways in which you can create new properties One is to add a prop erty column and insert values into it manually Another is to copy an existing property and modify the property values A third is to calculate one of a selection of new properties To add a property column to the Project Table choose Add from the Property menu In the Add Property panel you can specify the name the type and the initial value of the new property When you add the property all selected entries are assigned this property value Maestro 6 5 User Manual 95 Chapter 8 Projects Add Property Name vdW energy Type Precision 6 Initial value Figure 8 7 The Add Property panel If you don t specify a value the property is created but no values are assigned For real valued properties you can set the precision to which the value is displayed To create a new property by copying an existing property choose Copy from the Proper ties menu to open the Copy Property panel In this panel select the pro
124. duplicates The title is preserved when the copy is made 8 5 5 Merging Multiple Entries Maestro allows you to merge two or more selected entries while leaving the original entries unmodified To merge entries select the entries and choose Merge from the Entry menu The first new entry in a session is automatically named merge Subsequent combi nation entries are named merge mrg1 merge mrg2 etc When you merge entries Maestro places the new entry after the last entry that was included in the merge operation The new entry inherits the title from the first selected entry 8 5 6 Splitting Entries by Molecule Entries that contain multiple molecules can be split into entries that contain individual molecules For example you can split a protein ligand complex into separate entries for the protein and the ligand To split an entry select it and choose Split by Molecule from the Entry menu When an entry is split a copy of the original entry is kept and a new entry is created for each molecule in the original entry The exception is that water molecules are 90 Maestro 6 5 User Manual Chapter 8 Projects collected in a single entry with the suffix waters appended to the original entry name The new entries retain the same base name as the original entry with disn appended The number n indexes the new entries 8 5 7 Deleting Entries You can delete entries from the Project Table by selecting the entries then choosing Delete from
125. e symbols to distinguish the names To apply unique names to all atoms click Make Unique in the Modify existing names section As for canonical names you cannot selectively apply unique names 48 Maestro 6 5 User Manual Chapter 4 Building Structures 4 10 Changing Residue Properties Residue properties can be changed in the Residue Properties folder This folder is laid out in a similar fashion to the Atom Properties folder with a Property menu and a set of tools displayed for each choice The residue properties and their tools are described below In order to view the results you must first display the appropriate atom labels Residue Number To renumber residues in the Renumber Residues section enter the starting value in the Renumber From text box then use the picking tools to select the residues to renumber Renumbering a single residue is the same as assigning its number To apply a specific number to one or more residues in the Apply residue number section enter the number you want to apply in the Residue number text box then use the picking tools to select the residues to apply the number to Residue Name To name residues enter the residue PDB name in the Residue PDB name text box and use the picking tools to select the residues to name Build build Heiki ZZ IX ode Rf sl adah Atom Residue Fragments Properties Properties Property Residue Number Renumber residues Renumber from W Pic
126. e Color ramp option menu according to the value of the volume property on the surface The range of colors is determined by the range of values in the volume This scheme can be used for example to display the values of the electrostatic potential obtained from a Jaguar calculation on the van der Waals surface 134 Maestro 6 5 User Manual Chapter 11 Surfaces Isosurface Surface name Isovalue Isosurface Cancel Figure 11 7 The Isosurface dialog box 11 4 3 Creating Changing and Deleting Surfaces New surfaces To create a new surface from the existing volume data click New The New button opens the Isosurface dialog box and is only available when a volume has been selected An isov alue surface can only be created from a volume 3D grid of data The isovalue is the current value of the property that was used to create the surface Surfaces generated by Jaguar and Sitemap surfaces have volume data for which an isovalue can be specified Molecular surfaces van der Waals surfaces and extended radius surfaces do not have volume data Changing isovalues You can change the isovalue for an existing surface If the associated volume is present the Isovalue text box is editable If not it is read only To edit the value type a new number in the Isovalue text box The surface is redisplayed with the new isovalue Limiting surfaces You can limit the visible portion of the surface to the portion that is wi
127. e properly other windows must not overlap the Plot XY panel Two image formats can be selected from the panel TIFF and JPEG TIFF When Maestro saves an image as a TIFF file it uses no compression This means that the image is lossless all of the information in the original image is retained but the file can be quite large The TIFF format is recommended for saving high quality Maestro images JPEG JPEG is actually a compression method not an image format The JPEG file format speci fies a means of compressing natural images that doesn t severely impair the perceived image quality The JPEG method is almost always lossy meaning that the reconstituted pixel data differs from that of the original In Maestro the JPEG Quality parameter is fixed at 75 and the most common JPEG file format JPEG File Interchange Format JFIF is used 122 Maestro 6 5 User Manual Chapter 11 Surfaces The Maestro surface facility allows you to create and visualize molecular structure surfaces extended radius surfaces van der Waals surfaces and maps of active sites in receptor molecules to import surfaces and to display electrostatic potential surfaces density surfaces and molecular orbitals generated by Jaguar Some surfaces are constructed directly as a set of surface elements Other surfaces are derived from data for a function on a three dimensional grid This data is called a volume The surface is created by selecting a val
128. e Build panel toolbar or from the Atom Properties folder From the Set Element button menu in the toolbar A la you can choose an element from H C N O P or S then click on an atom in the Work space to change it to the selected element If you want to change an atom to some other element choose Element from the Property menu in the Atom Properties folder A periodic table is displayed from which you can select an element then click on an atom in the Workspace to change it to that element You do not need to select Set Element this is done automatically when you click on an Build build AXE ce adah Atom Residue Properties Properties Property Element a Fragments E Set element l Figure 4 3 The Atom Properties folder showing tools for the Element property 38 Maestro 6 5 User Manual Chapter 4 Building Structures element However you can select Set Element if it is unselected and you want to use the currently selected element 4 5 Changing the Bond Order and Formal Charge After creating a structure using the tools in the Build panel you may wish to change some of the bond orders or formal charges Tools for making these changes are available on the Build panel toolbar To increase the bond order click the Increment bond order toolbar button et then click the bonds whose order you want to increase Each click increments the bond order by one up to a maximum of three You ca
129. e Help Figure 9 1 The Distances folder of the Measurements panel To select atoms for measurement ensure that Add is selected choose Atoms or Bonds from the Pick menu in the Define atoms for measurement section and pick the atoms or bonds in the Workspace When you have picked the requisite number of atoms the measurement is made and entered into the measurement list If Show Markers is selected a dashed line indicating the atom locations and the numerical value obtained from the measurement is displayed in the Workspace Distances are marked in purple angles in green and dihedrals in red Once you have defined atoms for a measurement those atoms remained defined until you delete the atom set or remove the structure from the Workspace See Section 12 2 1 on page 138 for information about the user preference that affects this behavior If you only temporarily want to undisplay the results of your measurements deselect Show Markers However if you no longer need the measurement value itself you can remove it by selecting the corresponding list item and clicking Delete To delete all of the atom sets currently defined for a particular type of measurement click Delete All You can also delete measurements by picking select the Delete option and pick an atom in the measure ment you want to delete 104 Maestro 6 5 User Manual Chapter 9 Tools You can also make measurements using the Measure distances angle
130. e selected plots to their initial full scale setting of 100 zoom and no panning The final section of the zoom bar is the Zoom Box a control for directly setting the zoom and pan relative to an image of the plot s data This control is only active if you have a single plot selected If you have no plots selected or more than one plot selected this control is blank If the Zoom Box is active you can use it to display only a portion of the selected plot To change the current view of the plot click inside the Zoom Box to center the view on that location To zoom in drag the mouse The selected plot is zoomed to show only the rectangle defined by the mouse If you want to pan or zoom in on a single plot using the mouse you can use the Pan plot and Zoom box buttons in the tool bar 9 4 To pan a plot click the Pan plot button then drag the mouse in the plot in the desired direction The data follows the mouse movement To zoom in on a plot click the Zoom box button then drag the mouse over the region you want to zoom in on When you release the mouse button the plot zooms in to the defined region 10 2 3 Labeling and Unlabeling Data Points You can add labels to data points or delete them by clicking either the Label Points button or the Unlabel Points button which are shown below pe pe To label points click the Label Points button then click a data point The Label Points dialog box opens In this dialog box you can label the p
131. e spreadsheet file The values of the key that you choose in this column are matched to the values of the property that you choose in the Match to property in Project Table column For example if both the spreadsheet and the Project Table have a Title property you can match the rows by title If the file key value for a given row in the spreadsheet matches more than one entry the properties for that row are copied to all entries if several file key values match a single entry the row for the last file key value that matches is used to import data To complete the import choose the delimiter that is used in the spreadsheet file then click OK The values in the spreadsheet are imported into the Project Table Maestro 6 5 User Manual 29 Chapter 3 Importing and Exporting Structures and Data 30 Maestro 6 5 User Manual Chapter 4 Building Structures Maestro provides a variety of tools for building and modifying structures In the Build panel you can create molecular structures from predefined fragments or from individual atoms and modify structures and atom and residue properties Other panels enable you to add hydrogen atoms adjust the geometry connect or fuse molecules and define centroids of groups of atoms You can also set preferences for the behavior when certain building tasks are performed in the Preferences panel Some of the operations for building and modifying structures involve selection of atoms in the Workspace For i
132. ed but the case of the lt value gt is signifi cant So Program Jaguar is the same as program Jaguar but program jaguar would fail Parentheses can be used to group conditions but these must also be protected if used on the Unix command line For example to list all QSite jobs in your database that either died or were killed enter the command SSCHRODINGER jobcontrol list program QSite AND lt died OR killed gt If a job is stranded it might still be possible to re establish contact with the job and incor porate the results This can be done with the command SCHRODINGER jobcontrol recover jobid If this command fails however the job is cleaned up and the results are no longer avail able Maestro 6 5 User Manual 171 Chapter 14 Job Control 14 4 The Job Database Information about each job is kept in the user s job database which is stored in the direc tory SHOME schrodinger jobdb The database contains a record for each job You can determine what jobs are in the database by using the Maestro Monitor panel or the command line job control utility 14 4 1 The Job Record Each job has a job record in the job database The job record is a list of fields one on each line each consisting of a field name and its value Many of these fields contain informa tion that is only useful to the job control system but a number may also be useful to users Some of the latter are listed in Table 14 3 Table 14 3 Fields used
133. ed and retained when the files are read by Schr dinger products Maestro files are also self describing data items are named rather than simply identified by position and the data type string real number integer and Boolean is included as a single digit code letter at the beginning of each data name Since Maestro files can accept additional user defined fields it is not possible to give an all inclusive example of a Maestro file Instead this section will give a general overview of the Maestro file format and describe the components used for most Schr dinger appli cations A 1 Basic File Description Maestro format files are free format ASCII text All white space spaces tab characters end of lines etc is ignored Schr dinger applications will write files in a consistent layout in order to enhance human readability but the files are not in fact required to follow this layout Except for the requirement that string type data items which contain blanks be surrounded by double quotes there are no restrictions such as width or precision of the numeric fields on the data items A 2 Data Blocks The basic unit of a Maestro file is a block a series of data items contained within a pair of curly braces For instance the following is the first block of the example file in shown in this appendix Ss m m2io version 1 0 0 Most blocks in the Maestro file are proceeded by a name for example _m_ct where f stan
134. ed from Maestro are run under Schr dinger s job control facility The job control facility provides a uniform mechanism for launching monitoring and controlling calculations both for jobs launched from Maestro and for jobs launched from the command line The job control facility keeps information on jobs in a database that is set up for each user By default the job control facility allows you to run jobs locally However you can also run remote and in some cases distributed jobs and parallel jobs To run jobs run on a remote host you must first configure job control by editing your schrodinger hosts file and setting up any protocol needed to connect to the remote host 14 1 Configuring Job Control Configuration of job control is done in the schrodinger hosts file The default instal lation of this file is configured to allow running of jobs locally and no action is required by the user However if you wish to run distributed jobs run jobs remotely change the loca tion of the scratch directory or set up the remote environment then job control must be configured The following sections describe how to specify the scratch directory how to prepare your account for remote job submissions and how to modify the hosts file schrodinger hosts Information on configuring job control is also contained in the Schr dinger Product Installation Guide including configuration of batch queues 14 1 1 The Scratch Directory Most jobs now ru
135. ed job from the database dump show the complete job record help describes the job control commands kill terminate the job immediately killnooutput terminate the job immediately and discard the output list monitor n pause ping recover refresh resume show stop update list the JobId job name and status ask for monitoring files to be sent every n seconds suspend the job temporarily verify that a running job responds to job control messages try to retrieve results from a stranded job update the status of the job continue running a paused job show more details of the job status ask the job to stop itself as soon as possible Jaguar MacroModel only ask for an update of the job results MacroModel only of the machine on which the job was launched a sequence number and a hexadecimal timestamp e g mirabelle 0 alb2c3d4 The job status codes and their meanings are listed in Table 14 1 on page 168 The following examples illustrate different values of job selection To list all active jobs showing their JobIds job names current status and the machine on which each is running enter SCHROI To list all the j SCHROI To list just the SCHROI To list all jobs SSCHROI 170 job DINGER jobcontrol list jobs in your job database that finished successfully enter DINGER jobcontrol list finished whose Jobld is serv01 0 alb2c3d4 enter DINGER jobcontro
136. ein When you select Amino acids from the Fragments menu a Mutate button appears beside the Define grow bond picking tools To mutate a residue select Mutate select the new residue from the list and pick an atom in the residue you want to mutate The new residue replaces the old residue Maestro 6 5 User Manual 35 Chapter 4 Building Structures 4 2 2 Building Structures Using Grow Mode In Grow mode you can take advantage of the predefined grow rules that dictate where and how fragments are connected to build structures To enter Grow mode select Grow in the Fragments folder To create a structure in Grow mode click the fragments in the fragment library that you want to assemble in the Workspace At each click the selected fragment is added to the structure and a green arrow marks the location of the grow bond the bond that will be replaced when the next fragment is added To grow a structure from a location other than that indicated by the current grow bond you can choose a new grow bond using one of the following methods Choose Atom from the Pick menu of the Define Grow Bond section and pick two atoms in the order that defines the grow direction e Choose Bond from the Pick menu of the Define Grow Bond section and pick a bond The grow direction arrow points to the atom closest to where you click e Choose backward from the Grow Direction option menu The grow bond moves to the opposite end of the molecule In ad
137. element the element of the existing atom is not changed thus it does not matter which element is selected when you draw a bond between two existing atoms The atoms that you draw are placed in the x y plane If you want to create a 3D structure you can rotate the structure in the Workspace with the middle mouse button then continue drawing atoms Rotation does not change the active atom or exit Draw mode You can also move atoms that you have placed using the Move button menu B To move an atom in the x y plane choose X Y from the button menu click the atom you want to move then click the new location If the atom is in a ring only the atom is moved If the atom is not in a ring the atom and its attached atoms are moved To move an atom in the z direction choose Z or Z from the menu and click the atom to be moved The atom is moved 0 5 in the chosen direction Maestro 6 5 User Manual 37 Chapter 4 Building Structures 4 4 Changing Elements Whether you build a molecule in Place mode Grow mode or Draw mode the range of elements available to you is limited To include other elements in your structure you must first build with existing elements then change the element to another element in the appro priate locations in the structure You do not have to complete the structure before you make the change you only have to place an atom at the desired location Changing an atom from one element to another can be done from th
138. ent entry selection is all Intersect limits the selection of entries to those in the current entry selection that also meet the new criterion using a logical AND operation on the ESL expressions Entry Selection Select only these entries in Project Table Properties Filters Included State amidine Selected State acid y Is defined any value Subtract Hamide Subtract 4 In the range Hamine Intersect Hmetab gt Hrotor entries TEVEG Examples matching stars lt 30 1 3 0 ACKDNA 5 SA Range in table TT 0 2 ESL user stars gt 7 A Create Filter All Undo e 20 Clear Invert Matching 5 Entries OK Cancel Help Figure 8 4 The Entry Selection dialog box Maestro 6 5 User Manual 87 Chapter 8 Projects In addition to these three buttons the Invert button at the bottom of the panel inverts the entire current entry selection using a logical NOT operation All entries that were selected are unselected and all entries that were not selected are selected You can undo multiple operations with repeated clicks on the Undo button The Redo button reverses undo operations and can also be used multiple times You can also type ESL expressions directly into the ESL text box The hand edited expressions are consid ered part of the last operation performed with the mouse and can be undone and redone as part of that operation but cannot be undone or redone separately On
139. er right to lower left by choosing the corresponding items from the Display menu You can save the size and location changes in a layout file by choosing Save Panel Layout from the Maestro menu in the main window Maestro immediately saves your panel settings to the file named layout res in your preferences directory If you want to return the panels to their default sizes and locations delete the layout res file If you change the panel size and location during a session and want to revert to the last saved layout choose Restore Saved Layout from the Maestro menu 12 2 Setting Preferences The Maestro Preferences panel has seven folders each of which contains controls for modifying Maestro s default behavior according to your personal preference Changes made to interface settings in the Preferences panel are persistent they define Maestro s default behavior until you modify them A file called prefer cmd which contains all of your Maestro preferences is created and saved to your preferences directory To open the Preferences panel choose Preferences from the Maestro menu Maestro 6 5 User Manual 137 Chapter 12 Customizing Maestro Preferences prefer EEE Delete Markers Font Size Project Directory Label Mouse File suffix Builder When replacing but not editing or adding a structure Delete all markers if connectivity changes ww Delete any markers with missing atoms Figure 12 1 The Delete Mar
140. ere are many that you use frequently The controls on the Command Alias panel allow you to assign shorter names to these commands For example you might want to define the alias label for the labelatom command You can then use these aliases in commands typed in the Command Input Area To open the Command Aliases panel choose Command Aliases from the Maestro menu Defining a New Alias To enter a new command alias click New type the abbreviation that you wish to use for the command in the Alias Name dialog box and click OK In the Command Aliases panel enter the command in the Alias Definition box for the abbreviation you entered in the previous step Saving Aliases To save your aliases click Save The aliases are written to the file alias cmd in your preferences directory Once the aliases has been saved they can be used in any subsequent Maestro session If you wish to use an alias only for the current session it is not necessary to save the alias Changing an Existing Alias Maestro is shipped with a set of command aliases already defined and these can be edited or deleted To change an alias select the alias in the alias list then type a new alias name or definition in the appropriate box To delete an alias from the list select it and click Delete To delete all currently defined aliases click Delete All Alias name help Alias definition helpsearch New Save Delete Delete All Hide He
141. ere in the Project Table You can also rename properties by choosing Rename from the Property menu and editing the name in the Rename Property panel To delete a property choose Delete from the Property menu to open the Delete Property dialog box select the properties in the list and click OK You can choose multiple proper ties by shift clicking and control clicking the properties Rename Property propertyrename ETE Properties Figure 8 10 The Rename Property panel Maestro 6 5 User Manual 99 Chapter 8 Projects 8 7 4 Displaying Selected Properties If you want to limit the number of properties displayed you can select the properties to be displayed in the Show Property dialog box To open this dialog box choose Show from the Property menu You can select multiple properties in the Properties list by shift clicking and control clicking the list items Below this list is a set of tools for selecting properties Show All and Hide All select all properties in the list and clear the list respectively In the Property Family section you can select properties that were generated by one of the computational programs such as QikProp or user generated properties properties that you added Clicking Show or Hide in this section adds or removes properties of that family to or from the selection When you have chosen the properties click Show to change the Project Table display You can redisplay all properties by choosing Sho
142. es when you include or exclude an entry from the Workspace You can choose between Never which turns off automatic fitting Only for single entry which performs a fit only when there is a single entry in the Workspace and Always which performs a fit whenever an entry is included or excluded Maestro 6 5 User Manual 139 Chapter 12 Customizing Maestro Preferences prefer EEE Delete Markers Font size Project Directory Label Mouse File suffix Builder Synchronize workspace changes Opening projects Automatically Open last project on startup Y When approved W Show project table v Only when specifically requested Options for saving project on close Fit to screen when inclusion changes Y Less disk space slower Never More disk space faster gt Only for single entries gt Always Figure 12 3 The Project folder of the Preferences panel Opening projects You can choose to open the last project you were working on when you start Maestro This feature is particularly useful if you are working on one project over a period of time You can always open a specific project when you start Maestro by using the p option See Section 2 1 on page 3 for more information You can also choose to display the Project Table when you open a named project This is the default behavior but it does not apply to the scratch project Options for saving project on close When you open a project the initia
143. essages are equivalent to Maestro s dialog box warnings The message numbers are defined as follows 2 ERROR 1 WARNING O OK A fatal error occurred and no Maestro file was generated Check disk permissions and disk space A Maestro file was created but an error at or above the base error level was returned At the default base error level this value is returned when red or blue atoms are present and for orange atoms if the dupli cate CONECT record convention is not followed See Table 3 1 on page 21 for a description of the atom colors A Maestro file was generated without any errors at or above the base error level Maestro 6 5 User Manual 201 Appendix D Utilities Using Templates for Non Standard Residues The pdbconvert program has been supplied with connectivity and bond order informa tion for standard residues For non standard residues the program predicts connectivity but not bond order However if the connectivity and bond order information for a non standard residue is known it can be used to read in the PDB file Create a new file that contains a template with this information see example below TEMPLATE ALA D lE Qe NUNG antep CA cB 1 E A i CEA UHR CA T 1HB CB 1 2HB CB 1 3HB CB 1 A connectivity template must begin with TEMPLATE and end with a closing brace Each line in the template should specify two atom names followed by a bond order Templates
144. ete To delete all pairs click Delete All After all the atom pairs are selected click Superimpose Atom Pairs to superimpose the two structures If you want to compare more than two structures or if picking individual pairs is not prac tical you can superimpose atoms defined by an ASL expression To do so click Select and construct the expression using the tools in the Atom Selection dialog box or enter the expression in the Superimpose by ASL text box For example to apply the superposition operation to only carbon atoms type atom e C and press ENTER For more information on the Atom Selection Language see the Maestro Command Reference Manual The default action when superimposing structures is to apply a transformation to the entries then calculate the RMS difference in coordinates If you want to preserve the coor dinates of the superimposed structures select Calculate in place no transformation The RMS difference is then calculated without moving the structures This is a convenient way of obtaining RMS differences for ligand poses in a receptor for example 108 Maestro 6 5 User Manual Chapter 9 Tools If you do not use the calculate in place option you can separate the superimposed entries by clicking the Tile Entries button in the toolbar 2p ojo The entries are aligned in a grid but they are not returned to their original coordinates If you do want to return the structures to their original positions you must
145. ext area at the top of the panel The display is updated as the log file changes For some kinds of jobs such as MacroModel and Jaguar geometry optimizations the Workspace is updated with each new geometry as it is generated Most Maestro operations stop the monitoring of a job You can also exit monitoring mode by clicking Detach on the Monitor panel You can resume or begin monitoring a job at any time by selecting it from the list of jobs in the Monitor panel You can monitor any job that uses Schr dinger software from the Monitor panel The job control facility keeps a database of all your jobs on all hosts regardless of whether they were initiated from Maestro or from the command line Maestro 6 5 User Manual 167 Chapter 14 Job Control Monitor monitor El BI xi 12 7706 kJ mol 0 0500 kJ mol 426 4146 kJ mol 672 2284 kJ mol 0 0000 kJ mol 1 6819 kJ mol T E for cross checking 186 5532 kJ mol BatchMin normal termination 28 Apr 2004 12 21 47 Torsion Improper Torsion YDW Electrostatic Explicit Hydrogen Bonds Cross Terms real 0m2 5435 user 0m0 230s I 0m0 057s Monitor W Show jobs from current project only incorporated zone1 dyall Tutorials Qui ckTopi cs Bui l Figure 14 1 The Monitor panel If you want to monitor a job and the Monitor panel is not open choose Monitor Jobs from the Applications menu Every job proceeds through a series of well defined stages The current stage
146. f the job is not being monitored when it finishes you can open the Monitor panel from the Applications menu in the Main Menu Bar and monitor the completed job to incorporate the results Once the sitemap for a particular entry has been generated the surface information is incorporated into the Project Table and denoted in the Surf column for the entry with a button bearing the letter V To open the Surface Table panel and view the data associated with this surface click this button 130 Maestro 6 5 User Manual Chapter 11 Surfaces 11 2 6 Viewing the Sitemap Surface The sitemap is displayed as a pair of isosurfaces generated from the hydrophilic and hydrophobic grids The default isovalues 6 and 0 5 kcal mol can be changed in the Maestro Surfaces panel if more expansive or more restrictive philic and phobic volumes are appropriate in a given application If you need to see inside these surfaces you can display them as Mesh surfaces or if you display them as Solid surfaces the default you can increase the transparency 11 3 Importing Surface or Volume Files Using the Import Surface Volume File Selector you can read in either a Maestro vis file or a Jaguar plt file associate this data with a project entry and display the data as a surface To open the Import Surface Volume File file selector choose Import Surface Volume from the Surfaces submenu of the Display menu or click the Import button in the Surface Table panel I
147. fied by the environment variable SCHRODINGER TMPDIR on the remote machine e The directory specified by the environment variable TMPDIR on the remote machine If no other specification for tmpdir is found the directory HOME schrodinger tmp is used In this case the username is not used to form the scratch directory name since it would be redundant Environment variables on the remote machine are created in the normal manner for a remote shell command Note that environment variables are not created if the user s default shell is ksh In all cases tmpdir is created if necessary When the job finishes the scratch directory is automatically removed if the following conditions are met e The output files were all successfully copied back to the startup directory The directory did not exist before the job started 14 1 2 Preparing for Remote Job Submission To run remote or distributed jobs executing remote commands using the rsh or ssh command without specifying a password must be enabled This typically requires one of the following e Ahosts equiv file exists in the etc directory on each host This file should con tain a list of hosts amongst which users can log in without giving their passwords provided that their userids are the same on each of the machines Creating a hosts equiv file usually requires root permission e A rhosts file exists in the user s home directory on each of the remote hosts The rhosts file sh
148. he Open Project dialog box Show Hide project table Show the Project Table panel or hide it if itis displayed Create entry from workspace Create an entry in the current project using the contents of the Workspace Show Hide Build panel Show the Build panel or hide it if it is displayed Local transformation Pick the object to transform Menu but ton with a pick menu and an item to open the Advanced Transformations panel Fit to screen Scale what is displayed to fit into the Workspace and reset the center of rota tion Set fog display state Menu button Automatic means on when there are more than 40 atoms in the Workspace off when there are fewer Rotate around X axis by 90 degrees Q Import structures Show the Import panel Save as Open the Save Project As dialog box to save the project with a new name Delete Choose an object to delete Menu button with a pick menu a section to delete hydrogens and waters and to open the Atom Selection dialog box and a sec tion to delete other objects associated with the structures in the Workspace Add hydrogens Pick atoms for hydrogen treatment Menu button with a pick menu and an item to open the Atom Selection dialog box Undo Redo Undo or redo the last action Performs the same function as the Undo item on the Edit menu and changes to an arrow pointing in the opposite direction when an Undo has been performed indicating that its next action is
149. he Tools menu To superimpose all the displayed structures click All in the Superimpose by ASL section The superposition is done using the atom numbers This option is useful if each entry has the same number of atoms and is numbered the same way which usually requires that the entries be conformers If the structures you want to compare are not conformers or if you only want to compare part of the structure you can select the atoms to superimpose To compare two structures you can select the atoms to superimpose in each structure in pairs To define the atom pairs select Pick atom pairs then pick the atom pairs You must pick one atom from each entry and you must pick the first atom from the same entry each time The atom pairs are displayed in the Superimpose by atom pairs text box as you pick them If Show markers is selected the atom pairs are connected by dashed lines Once you have picked the first pair Superimpose Atom Pairs Delete and Delete All are activated If Maestro 6 5 User Manual 107 Chapter 9 Tools ijmix Delete Delete All W Pick atom pairs E Show markers Superimpose Atom Pairs Superimpose by ASL Clear AII Select LI J Calculate in place no transformation Create property for included entries RMSD Mols 2 1 RMS 0 7782 Maximum Ca a Hide Help Figure 9 3 The Superposition panel you need to delete a pair select the pair in the list and click Del
150. he project so they are persistent 80 Maestro 6 5 User Manual Chapter 8 Projects Project Table table test Table Select Entry Property ePlayer ti Aya Be Bo Tel R lt DDI 2 selected ferret 0904 5 mol_0004 impt__ fo o Qo mol 0004 mol 0004 impi inci O 0 gt mo1_0007 mol 0007 imi 2 jo 14 Q mol 0007 mol 0007 impicinct t fo 5 S gt fmo1_o008 mol 0008 im fo jo mo _0008 mo1_o008 impi inc1ifo 0 Omol 0018 mol_oote impt jo jo An included An excluded A fixed or Selected entry entry locked entry entries Figure 8 2 The Project Table panel 8 3 1 The Project Table Toolbar The toolbar contains two groups of buttons and a status display The first set of buttons opens various panels that allow you to perform functions on the entries in the project table The second set of buttons controls the ePlayer which plays through the selected struc tures each structure is displayed in the Workspace in sequence at a given time interval A description of the toolbar buttons is provided below The use of these buttons is also discussed in later sections of this chapter Find Open the Find panel to locate alphanumeric text in any column of the Project Table except for the row number Sort Open the Sort Project Table panel to sort entries by up to three properties Plot Open the Plot XY panel to p
151. he title or the entry name You can swap these two from the Columns submenu of the Table menu 84 Maestro 6 5 User Manual Chapter 8 Projects BETE Find text 4 Match case Direction Match whole word only Up Down Hide Help Figure 8 3 The Find panel Setting the precision of real values You can set the precision of real valued properties in the Set Precision dialog box which you open from the Property menu 8 3 6 Finding Text in the Project Table If you want to locate some text in the Project Table whether it is a string or a numerical value choose Find from the Table menu The Find panel is displayed Enter the text you want to find select any options and click Find The Project Table scrolls to the found entry but the entry is not selected 8 4 Selecting Project Entries Selection is the action of choosing entry rows in the Project Table which become the target for an action The rows are highlighted when they are selected Selection differs from inclusion which is the display of the structures belonging to entries in the Work space Inclusion is described on page 80 Selection is no different in principle from the selection of items in a list in any graphical interface In addition to the usual mouse opera tions summarized in Table 8 1 Maestro provides additional capabilities for selecting entries based on their properties Once entries are selected they can be operated on using
152. hey become invisible Maestro 6 5 User Manual 133 Chapter 11 Surfaces Drawing Color Scheme Drawing Color Scheme Isovalue 0 010000 didi ww Constant color W Displayed D Negative color co Transparency 4 Map values from volume data Style Solid a carboxyindole 01 plot density carboxyindole 01 plot potential Color ramp Red White Blue Figure 11 6 The Drawing and Color Scheme folders of the Surface Table panel 11 4 2 Selecting a Color Scheme You can color a surface with one of three schemes coloring by the values of a property coloring with a constant color or coloring with the values of a volume on the surface These schemes are selected in the Color Scheme folder Color by Property When you choose to color by a property value each part of the surface is colored according to the value of the property on the nearest atom to that part of the surface Constant Color If you want to apply a constant color choose the desired color from the Constant color option menu When a surface has both positive and negative portions as with orbitals the Negative color option menu is active and you can select the color in which the negative surface is displayed Color by Volume Data You can color a surface using the property data in a volume which you select in the list under Map values from volume data The color fades between the colors selected in th
153. ibbons the use of some color schemes and for the Workspace sequence viewer 112 Maestro 6 5 User Manual Chapter 10 Plotting Maestro s Plot Facility allows you to generate XY plots of any two columns of data in the Project Table Multiple plots are supported and plot data is stored inside the project When you have created a plot you can select data points in the plot and display the corre sponding entries in the Workspace 10 1 Creating Plots Plots are created from property data in the Project Table To plot data you must therefore have at least one entry in the Project Table To create a new plot first select the entries in the Project Table whose data you want to plot then choose Plot from the Table menu or click the Plot button on the toolbar a esa The Plot XY panel is displayed with a blank plot area Now choose New Plot from the Plot menu The New Plot dialog box is displayed To assign a name to the plot enter a name in the Plot Name text field The name appears in lists used to select plots in the caption name underneath the plot and in any TIFF or JPEG images that you make of the plot You can plot more than one set of data in a single plot To distinguish the data sets or series enter a name in the Series Name text field To create new series however you must use the New Series dialog box See Section 10 3 2 on page 119 for more information When you have assigned names choose the property to be plotte
154. icitly save the project When you have finished working in a project you need only close the project by choosing Close from the Project menu If you want to work on a different project you do not need to close the old project before opening the new project When you close a project without opening a new project a scratch project is created If you are working in a scratch project and decide you want to save it as a named project or if you want to save a named project with a different name choose Save As from the Project menu or click the Save As toolbar button Ea A project selector panel is displayed that enables you to enter the name and choose the location of the project and if necessary create a directory The panel is described in Section 8 1 4 on page 77 If you choose Close when you are working in a scratch project you are prompted to save the scratch project 8 1 3 Deleting Projects If you do not want to keep the current project you can remove it by choosing Delete from the Project menu You will be prompted to confirm the deletion of the project When you delete a project any jobs associated with that project are killed and purged from the job database You can also delete the project from a Unix shell by entering the command rm rf project name When you delete a project using rm job files that were created using the project are not deleted unless they are located within the project directory 76 Maestro 6 5 User Manual
155. iguring the Project Table display and behavior The Select menu Provides commands and access to the Entry Selection dialog box and Filter panel so that you can select entries 82 Maestro 6 5 User Manual Chapter 8 Projects The Entry menu Provides tools for including and excluding entries controlling the display of entries in the Project Table and performing various operations on the selected entries The Property menu Provides tools for displaying and manipulating properties The ePlayer menu Provides access to the play controls and the ePlayer options 8 3 3 Mouse Functions in the Project Table The standard use of shift click and control click to select objects is supported in the Project Table This behavior applies to selection of entries and inclusion of entries in the Workspace Dragging to resize rows and columns and to move rows is also supported You can drag a set of non contiguous entries to reposition them in the Project Table see Section 8 5 8 on page 91 for more information You can edit cells by clicking in the cell and changing the text then pressing ENTER or clicking elsewhere in the Project Table A summary of project based mouse functions is provided in Table 8 1 Table 8 1 Mouse operations in the Project Table Task Mouse Operation Change a Boolean property value Display the Entry menu for an entry Display a version of the Property menu for a property Edit the text or the value i
156. ile used for a given job is the first one found in the following list 1 The file specified by the environment variable SCHRODINGER_HOSTS 2 The schrodinger hosts file in the current directory 3 The schrodinger hosts file in SHOME schrodinger 4 The schrodinger hosts file in SCHRODINGER For distributed MacroModel jobs the following locations are searched first E 1 A file specified by the command line argument HOSTFILI 2 The file jobname hst in the startup directory on the startup host where jobname is the stem of the command file name for the current calculation e g 1f the command file were called ca1_en1 com this file would be called cal_en1 hst Maestro 6 5 User Manual 163 Chapter 14 Job Control The schrodinger hosts file can be tested using the command SSCHRODINGER hunt rtest This command tests the first schrodinger hosts file found in the list above excluding the one specified by HOSTFILE This command also attempts to contact each of the hosts listed and thus also serves as a check on host accessibility and on whether rsh has been set up appropriately on the various hosts A sample schrodinger hosts file is shown below Schrodinger hosts file name localhost schrodinger software schrodinger name ahost name bhost name old_bhost host bhost schrodinger software schrodinger_old name another_host processors 2 tmpdir scr schrod
157. in the job record Field Name Meaning BackendPid The PID for the program carrying out the calculation Command The command used to start up the actual calculation Dir The startup and output directory on Host Envs Environment variable settings for the job Errors Error messages from the job control system ExitStatus The reason the calculation stopped Host The machine from which job was launched InputFiles Files copied from the output directory to the job directory at startup JobDir The directory in which the job is run JobHost The machine on which the job is run JobId The job s Jobld JobPid The PID for the job s jmonitor process JobUser The user name under which the job is run LaunchTime The time at which the job was submitted LogFiles Monitoring files that grow throughout the job MonitorFiles Files copied from the job directory to the output directory during monitoring MonitorInterval The interval sec between monitoring updates 0 if off 172 Maestro 6 5 User Manual Chapter 14 Job Control Table 14 3 Fields used in the job record Continued Field Name Meaning Name The job name OutputFiles Files copied from the job directory to the output directory at exit ParentJobld The Jobld of the parent job if this is a subjob Processors The number of processors used for a parallel or distributed job Program The program name Project The project name StartTime The time at which the calculation started running Status The curren
158. ing because the structures are imported into the current project Any structures that do not exist as entries in the current project are external to the project and therefore must be imported Similarly the term exporting is used instead of writing because a file is created for use outside the current project Data that is associated with structures can also be imported and exported independently to spreadsheet files This capability enables properties that are created by Schr dinger soft ware to be read by a spreadsheet program manipulated and re imported into the project 3 1 Importing Structures Structures are imported using the Import panel You can import data from files in Maestro MacroModel PDB Sybyl Mol2 MDL SD and a range of other formats If the files contain multiple structures such as the output of a conformational search you can select the structures to import When importing structures Maestro places each structure into a separate new entry in the current project For the Maestro file type molecular representa tion information can be imported along with a structure You can undo the import opera tion but the changes made to the Project Table remain To open the Import panel do one of the following e Choose Import Structures from the Project menu on the main menu bar Choose Structures from the Import submenu of the Table menu in the Project Table panel e Click the Import structures button on the main toolba
159. inger usr bin share schrodinger End of Schrodinger hosts file The hosts file consists of one or more entries each of which describes a host on which jobs can be run There is usually a single entry for each machine on which you want to run jobs For each entry in the schrodinger hosts file the following settings can be made name entry label host machine name user username tmpdir tempdir processors number of processors schrodinger installation path env environment variable assignment The settings are described in the following sections A full list of settings including settings for batch queue configuration is given in the Schr dinger Product Installation Guide 164 Maestro 6 5 User Manual Chapter 14 Job Control The settings can be formatted with any combination of spaces and tabs but the entire setting must be on one line Any number of comments can be included in the file Comments should start with a hash sign If you have installed Schr dinger products on multiple hosts you may need to edit the schrodinger hosts file on each host to add entries for the other hosts The name and host Settings The name setting must be the first line for each machine This is the name that is displayed in the list of known hosts in the menus of the product panels Usually entry label is the name of a machine a host that can be used to run a calculation but if it is not you must include a host setting that su
160. ion 14 1 1 on page 161 for more information on scratch or temporary directories You can override the tmpdir setting in the schrodinger hosts file by setting the SCHRODINGER_TMPDIR environment variable For example if the directory designated Maestro 6 5 User Manual 165 Chapter 14 Job Control by tmpdir becomes full with files that you don t have permission to delete you can set SCHRODINGER TMPDIR to a different directory and continue to run Jaguar jobs The processors Setting For stand alone computers with multiple processors set processors to the number of processors in the computer For computer clusters set processors for each node to the total number of processors in the entire cluster The schrodinger Setting The schrodinger setting specifies the directory in which your Schr dinger software is installed on this host This setting allows you to choose between versions of our software to use on the remote machine if more than one version is installed The schrodinger setting is also useful if your default shell e g ksh does not set the SCHRODINGER envi ronment variable on remote machines when using rsh or ssh You can provide multiple schrodinger settings for a single host entry You can override the schrodinger setting with the VER and REL options if you run a program from the command line See Section 14 5 on page 174 for details The env Setting The env setting specifies an environment variable that is t
161. ion from the right side of the folder The available conditions depend on the property type For some conditions you must enter a value or a range of values The avail able conditions are The property is defined For numerical real or integer properties the value lies in a given range for exam ple gt 5 0 or 1 7 You can use any of the six operators lt gt lt and gt to define the range of property values 86 Maestro 6 5 User Manual Chapter 8 Projects e For textual properties the text matches a given string Match means that the string given is contained in the property value The string can include the wildcard charac ters which matches any number of characters which matches any single charac ter and which matches any single digit For Boolean properties the value is true or false In addition the inclusion state and the selection state of the entry can be used as criteria To combine this criterion with the current entry selection click one of the buttons to the right of the panel Add adds entries that meet the new criterion to the current entry selection using a logical OR operation on the ESL expressions This is the default action which is per formed if you press ENTER e Subtract excludes entries that meet the new criterion from the current entry selection using a logical AND NOT operation on the ESL expressions If this is the first opera tion the default curr
162. ions click Save Saved macros are placed in the maestro mac file in your preferences directory To delete a macro edit this file Maestro 6 5 User Manual 155 Chapter 12 Customizing Maestro 156 Maestro 6 5 User Manual Chapter 13 Printing and Saving Workspace Images In addition to creating Maestro MacroModel PDB Sybyl Mol2 and MDL SD structure files Maestro can produce high quality print and electronic representations of structures depicted in the Workspace You can use the tools in the Print panel to generate PostScript and Encapsulated PostScript files and use the Save Image panel to create TIFF and JPEG images For information on writing exporting structure files see Chapter 3 13 1 Printing an Image File or Printer From the Print panel you can print or create PostScript or Encapsulated PostScript images of structures currently rendered in the Workspace To open the Print panel choose Print from the Maestro menu The settings available in the Print panel are described below Print To To print an image select Printer To write a PostScript PS or encapsulated PostScript EPS file select File File Format If you selected Printer in the Print To section only the Postscript PS option is available because you cannot directly print encapsulated postscript If you selected File select Post script PS or Encapsulated PS EPS Orientation Select Portrait or Landscape to determine the orientation of the im
163. iple files You can import structures from more than one input file at a time To select multiple input files use the SHIFT and CTRL keys in combination with mouse clicks to select as many files as you wish in the Files list or click All Files to select all files in the Files list 3 1 2 Selecting Import Settings Once you have selected the files to import structures from you must choose which struc tures to import and how to display them Selecting structures to import Maestro can import multiple structures from multiple files If you do not want to import all structures from each file deselect Import all struc tures You can then enter the index of the first structure in the Start text box and the total number of structures to import in the Total text box You can import to the end of the file by selecting End instead of specifying the total number These settings are applied to all files they cannot be set for each file in a multiple file selection To import different numbers of structures from a set of files select each file in turn and set the number of structures to import Selecting structures to display When you import structures from a file you can set options to control which structures to display and whether the structures already in the workspace are cleared or not If Replace workspace is selected the default setting Maestro automatically clears existing structures from the Workspace To import new structures without rem
164. irst two tool types you can also select items by picking in the Workspace For example if you choose the Element property in the Atom category then picking a carbon atom in the Workspace selects the C item in the list of elements If Show Markers is selected the atoms that are selected by the definition of a property and its allowed values are marked in purple in the workspace After each selection these markers are updated and the value in the Atoms Matching field is updated to report how many atoms are matched by the current property specification 5 2 2 Combining and Modifying Atom Selections When the selection is complete you can combine it with the previous selection The Add Subtract and Intersect buttons combine the ASL expression for the current selection with the existing ASL expression in the ASL text box as follows e The Add button includes the current selection in the existing selection by performing a boolean OR operation on the ASL expressions e The Subtract button excludes the current selection from the existing selection by per forming a boolean AND NOT operation on the ASL expressions The Intersect button restricts the selection to the atoms that are in both the current selection and the existing selection by performing a boolean AND operation on the ASL expressions In addition to combining ASL expressions to form a new selection you can negate an entire expression with the Invert button select all atom
165. ith the entries corresponding to the selected series click Make Series The Selection 10 3 3 Changing X and Y Axis Display The X Axis and Y Axis folders contain tools that allow you change the names scales and display status of the x and y axes respectively You can display more than one x axis or y axis on each plot Selecting an Axis The X Axis and Y Axis lists display all of the axes that exist in the selected plot You can select an axis from the list and change its characteristics Informa tion on the selected axis is displayed at the bottom of the folder Creating an Additional Axis To generate additional axes for the selected plot click the New button and set the controls in the dialog box that is displayed Click New to generate the new axis Editing Axis Definitions To edit the title minimum and maximum values and number of scale markers for the X and Y axes click the Edit button set the controls in the dialog box that is displayed and click Edit to implement your changes Deleting an Axis To delete an X or Y axis select the axis from list and click Delete Displaying and Undisplaying an Axis To display or undisplay an X and Y axis select the axis from the list select or clear the Display button 120 Maestro 6 5 User Manual Chapter 10 Plotting Plot Settings plotxysettings ETE Plot Settings plotxysettings EEE Piot Series X Axis Y Axis X Axis ew Edit Delete W Display
166. ities UNIX conventions are used for the command syntax see Chapter 1 for more information D 1 Structure Conversion This section describes the utilities available for conversion between various file formats for molecular structures These utilities are used by Maestro for structure conversion when importing or exporting structures D 1 1 Conversions to and From MacroModel Format maemmod Convert files from Maestro format mae to MacroModel format dat Syntax maemmod maestro file mmod file mmodmae Convert files from MacroModel format to Maestro format Syntax mmodmae mmod file maestro file mmio convert Compress and uncompress MacroModel format files Syntax mmio convert infile outfile Maestro 6 5 User Manual 199 Appendix D Utilities D 1 2 Conversions to and From Mol2 Format mmodmol Convert files from MacroModel format to Sybyl Mol2 format Syntax mmodmol input file output file If the input file is not specified input is taken from standard input Likewise if the output file is not specified output is sent to standard output Example mmodmol myfile dat gt myfile mo12 molmmod Convert files from Sybyl Mol2 format to MacroModel format Syntax molmmod input file output file If the input file is not specified input is taken from standard input Likewise if the output file is not specified output is sent to standard output Example cat myfile mo12 molmmod gt myfile da
167. ity propfilter extracts structures from a Maestro formatted file based on values of properties maesubset Extract a subset of structures from a Maestro format input file Syntax maesubset n range full mae gt subset mae maesubset h v range 1 200 structures 1 through 200 50 structures 50 through end of file bs c structures 1 through 5 and 14 Maestro 6 5 User Manual 203 Appendix D Utilities Options h Show usage summary v Show the version number of this utility sdsubset Extract a subset of structures from an SD format input file Syntax sdsubset n range full sdf gt subset sdf sdsubset h v range 1 200 structures through 200 50 structures 50 through end of file ns AM structures 1 through 5 and 14 Options h Show usage summary v Show the version number of this utility propfilter Filter Maestro formatted input file based on properties Can filter on QikProp property names or internal Maestro property names Syntax propfilter options input file propfilter h n v Options e filter condition A single filter condition Multiple such conditions may be speci fied filter file Input file listing filter conditions to be used h Show usage summary n List the recognized property names The input file is not processed 204 Maestro 6 5 User Manual Appendix D Utilities o output file Filename for output Maestro formatted file If no outp
168. ix Builder Maestro s current font size is Small Select one of the font sizes below The change will not take place until you restart the program Medium Large Figure 12 2 The Font Size folder of the Preferences panel 12 2 3 Setting Project Synchronization and Storage Preferences The Project folder of the Preferences panel contains a number of options for saving modi fications of a Workspace structure to the corresponding project entry saving projects and opening projects Synchronize workspace changes When you include an entry into the Workspace you are working with a copy of the struc tures in that entry By default Maestro saves or synchronizes changes in the Workspace version of the structure to the entry with which it is associated when you make the changes The other two synchronization preferences allow you to dictate what changes are saved to the project If you select When approved by user you are prompted to save Work space changes when you attempt to exclude that entry from the Workspace If you choose not to synchronize your changes are lost If you select Only when specifically requested Maestro does not prompt you to save changes made to Workspace structures you must click the exclamation point icon in the status bar to save any changes Fit to screen when inclusion changes In this section you can set preferences for when an automatic fit to screen is performed The action only appli
169. ject Table Changes 121 10 5 Saving Plot Images ueteri treno PE IRURE NOTE qua Ra SERERE 122 vi Maestro 6 5 User Manual Contents or CNET i c Henn 123 11 1 Generating SUCES i He ieri cec ste di 123 11 1 1 Surface Generation Controls munici ai 123 11 1 2 Molecular Structure SUTTACeS ie irr rtr tete pea 125 11 1 3 Extended Radius SUrtates iier rer aio 125 11 1 4 van der Waals SWEEACGR icon cta ceret tet lere ii 126 112 MAPS EST 127 11 25 Background meca Rr ala 127 11 22 Mapping Alcores t eet dolce 128 11 2 3 Specifying a Structure to Be Mapped 4 net 129 11 2 4 Defining the Mapping BOx eee 130 112 5 Ruins th Sitemap Job eed err 130 11 2 6 Viewing the Sitemap SU ii Lap ee eee 131 11 3 Importing Surface or Volume Files eerte nici tete 131 114 The Surtace Table Patel 2e dr teer e etr er eee eris 132 11 4 1 Changing the Appearance of the Surface sss 132 11 4 2 Selecting a Color Scheme crisol 134 11 4 3 Creating Changing and Deleting Surfaces n 135 1144 Imporine Siffates sso iano 136 Chapter 12 Customizing Maestro cssscccsscssscsscecsssccssccsssssccsscessesssecees 137 12 1 Changing and Saving Panel Layout 137 12 2 Setting Preferences incedere ad 137 12 2 1 Deleting Markers Upon Connectivity Change 138 12 2 2 Changing Font Size for Interface Component Text
170. k Chains an Select Apply residue number Residue number 1 Pick Residues a All Select Figure 4 12 The Residue Number tools in the Residue Properties folder Maestro 6 5 User Manual 49 Chapter 4 Building Structures Chain Name You can assign a single letter name to chains The definition of a chain is not restricted to the items labeled Chain in the pick menus you can define a chain in any way that you like and assign it a name To assign the name enter a character in the Chain Name text box and use the picking tools to define the chain 4 11 Defining Dummy Atoms Dummy atoms are used by several of the computational programs for defining geometries and geometric parameters You can retype an atom to a dummy atom type using the MacroModel Types atom property described earlier You can also place a dummy atom at the centroid mean position of a group of atoms such as a ring You can then change the dummy atom to a real atom and thus place real atoms at the centroid of some system of interest The centroid capability is available in the Centroids panel which you open from the Build menu To define a centroid select Pick atoms to define centroid pick the atoms in the Workspace The atoms are listed in the Atoms to define centroid list If you have Show markers selected the atoms are marked with a salmon colored star and the atom that is selected in the list is marked with a lavende
171. kers folder of the Preferences panel 12 2 1 Deleting Markers Upon Connectivity Change Markers are graphical symbols such as lines arrows and icons which indicate that the marked atoms or bonds have been selected for some type of operation such as measuring or defining constraints In the Delete Markers folder of the Preferences panel you can specify how you would like Maestro to treat markers when you are replacing one structure with another You may choose to delete markers when the atoms they mark are deleted or to delete markers only if the new structure has different connectivity between marked atoms The default behavior is to delete markers if the connectivity changes This allows measurement markers to remain present when a displayed structure is replaced by a conformer 12 2 2 Changing Font Size for Interface Component Text The Font Size folder of the Preferences panel allows you to change the font size of the text that is displayed in the GUI Changing the font size may change the amount of space each Maestro panel or window requires To select a new default font size click Small Medium or Large The actual point size depends on the size of your monitor screen The default is Medium After you have made your selection restart Maestro to implement the change 138 Maestro 6 5 User Manual Chapter 12 Customizing Maestro Preferences prefer EEE Delete Markers Font size Project Directory Label Mouse File suff
172. l 8 4 2 The Entry Selection Dialog Box The Entry Selection dialog box Figure 8 4 enables you to select entries in the Project Table based on a combination of criteria for property values Once you have defined a set of criteria for selecting entries you can store this set as a named filter and use the filter directly from the Select menu You can open the Entry Selection dialog box from the Select menu or using the Select Only toolbar button N The Entry Selection dialog box is similar in design to the Atom Selection dialog box It allows you to select entries using GUI tools rather than entering an ESL expression At the top of the entry selection dialog box is a title bar which defines the action to be taken when you click OK In the center are two folders Properties and Filters that you use to define property based criteria for entry selection or choose named filters to combine with the entry selection that is being created the current entry selection On the right are buttons for combining the criterion or named filter with the current entry selection These tools become available when you have selected a property and a condition for that prop erty or a named filter In the lower portion of the panel is an ESL text box that displays the current entry selection and a set of buttons for editing the current entry selection To define a property criterion choose a property from the list in the Properties folder then select a condit
173. l list serv01 0 alb2c3d4 in your database with the job name myj ob enter DINGER jobcontrol list myjob Maestro 6 5 User Manual Chapter 14 Job Control To list all jobs in your database enter SSCHRODINGER jobcontrol list all You can also use the wildcard character to match a single unspecified character or to match zero or more unspecified characters If you use either of these characters you must protect them to ensure that they are interpreted by the jobcontrol script and not the UNIX shell For example you could enter either of the following commands to list all jobs whose job names start with docklig SSCHRODINGER jobcontrol list docklig SSCHRODINGER jobcontrol list docklig More general queries are also possible Formally a query consists of one or more condi tions optionally separated by the Boolean operators AND OR or NOT If the operators are omitted OR is assumed A condition takes the form lt field gt lt op gt lt value gt where field is one of the field names in the job record and op is one of the following equals l is not equal to matches l does not match Equals means an exact match matches means the string lt value gt is found The field names are listed in Table 14 3 on page 172 The fields that are most likely to be useful for queries are Name Program Host Dir JobHost JobDir Project Status and ExitStatus The case of the field names is ignor
174. l state is stored in compressed format and the working copy is stored in uncompressed format When you close a project the initial state is replaced with a compressed version of the current state of the project You can choose to keep or to remove the uncompressed current state by selecting one of the following options Less Disk Space slower The uncompressed version is removed When you open the project again the compressed initial state must be uncompressed before it is read This option is useful if storage space is an issue More disk space faster The uncompressed version is kept When you open the project again the uncompressed version is read Prior to the Maestro 5 1 release projects were only stored in uncompressed format When you open a project from a previous release a copy of the project is compressed and stored as the initial state 140 Maestro 6 5 User Manual Chapter 12 Customizing Maestro Preferences prefer Delete Markers Font size Project Directory Label Mouse File suffix Builder Default directory for job startup and file i o 4 Maestro s current working directory w Parent of project directory w Project directory y Project jobs directory ww Other specify below Directory currentdir Figure 12 4 The Directory folder of the Preferences panel 12 2 4 Specifying a Default Working Directory The Maestro working directory is the directory to which file and project se
175. lace pre existing entries of the same name e Ignoring Output Output files are written to the working directory but structure and property data are not incorporated into the Project Table You can import the results later using the Import panel See Chapter 3 for more information on importing struc tures Incorporation of job output into the project takes place only from monitoring mode If you are monitoring a job launched from the current project and that job finishes during the monitoring session incorporation is immediate If you are not in monitoring mode when 176 Maestro 6 5 User Manual Chapter 14 Job Control the job finishes you must select and then monitor the job before the results are incorpo rated When a job is incorporated the first structure in the job output is displayed in the Work space Incorporated entries are in a contiguous block and the entry list is scrolled to the first of these entries Incorporation can be undone Undoing incorporation removes the new entries from the project and restores the Workspace to the state it was in just before monitoring mode was entered Computational programs normally propagate entry names as well as other properties from their input into their output structures Where the relationship is one to many as in a conformational search consecutive structures in the output file have identical entry names Tf the job is run with the append incorporation mode the names a
176. laced at the end Sorting these entries in ascending order places included entries at the end of the list To sort entries by a single property right click and hold in the property header and choose Sort from the menu that is displayed To sort entries by more than one property you can use the Sort Project Table panel In this panel you can choose from three sort keys to sort the entries and for each key you can choose to sort in ascending or descending order Maestro 6 5 User Manual 91 Chapter 8 Projects Sort Project Table tablesort ENE Secondary Key none none Hacid acid Hamide fami de fami dine fami dine Hamine Hamine Hamine Hinetab metab metab rotor rotor rtvFG HrtvFG stars stars stars ACKDNA 5 SA Z ACKDN4 5 SA 7 Order Ascending Order Ascending Order Ascending Sort Selected Rows Sort All Rows Hide Help Figure 8 5 The Sort Project Table panel To sort entries 1 Select the desired entries 2 Choose Sort Selected Entries from the Table menu or click the Sort toolbar button A zw The Sort Project Table panel is displayed 3 Select a property from the Primary Key list 4 If you want to sort entries whose primary key is the same by another property select a property from the Secondary Key list and likewise for the Tertiary Key list 5 Select Ascending or Descending for each key for which you made a selection 6 Click Sort Selected Rows or Sort
177. le The formats for which Maestro recognizes the extension are Maestro Mol and Mol2 PDB SD XYZ Mopac Cartesian and Internal and Spartan This option is useful if you want to locate any of these kinds of structure files Selecting a directory To specify the directory from which to import you can enter it in the Path text box navigate to it using the Directories list or click Launch Directory or Current Directory to select the directory from which you launched Maestro or the current working directory The path and the directory and file lists are updated for the chosen directory Selecting a file To select a file you can type its name and path in the Selection text box or select it from the Files list Maestro 6 5 User Manual 19 Chapter 3 Importing and Exporting Structures and Data If you selected one of the four specific file types from the first section of the menu or some of the Babel file types the file that you select must have the correct extension If you type the name of the file in the Selection text box you must include the correct extension In the Files list only files with the correct extension are displayed Tf the file does not appear in the list check that you have chosen the correct file type in the Format section or select All in the Format section to view all files You can also view files with a different extension by altering or deleting the filter and pressing RETURN or clicking Filter Selecting mult
178. le menu and are discussed in detail in Section 3 3 on page 26 and Section 3 4 on page 28 To specify a filename for the exported data type a name in the File text box To export the file to Maestro s current working directory click Export To export to a different directory click Export To and navigate to another directory 8 8 Undoing Project Operations All changes made directly to the Project Table are saved immediately regardless of your synchronization preference setting The synchronization setting affects only the changes made in the Workspace For more information about synchronization preferences see Section 12 2 3 on page 139 You can save a copy of your project using Maestros Snap shot feature before performing operations that you might want to undo To generate a snapshot of the current project choose Make Snapshot from the Project menu If the synchronization mode you have selected is When approved by user and you have modified entry structures in the Workspace but have not synchronized the changes you may be prompted to do so Otherwise the Make Snapshot command is executed immedi ately and you receive no notification other than the temporary display of the cursor as a stopwatch Only one snapshot can be preserved at a time Any previous snapshots are overwritten when you issue the Make Snapshot command To revert to the snapshot you made choose Revert to Snapshot from the Project menu If you want to discard all
179. lea aa aa 18 3 1 2 Selecting Import Settings iii 20 3 1 3 Error Reporting for PDB Files eerte 21 3 1 4 Entry Naming Conventions for Imported Structures 22 3 1 5 Reading Jaguar Input FileS errar 22 3 2 Exporting Stc eS TH EE 23 9 2 Selecting Export Settings ciglia 24 3 2 2 Exporting Multiple Pies eerte eere tert rtr 25 3 3 Exporting Data to Spreadsheet ce ette temer nete 26 34 Importing Data from a Spreadsheet ceteri caritas 28 Chapter 4 Building Structures eee eee ee eee ee eee eee eene te sete sete sense tna e ena 31 4 1 The Build Panel air 31 4 2 Building a Structure From Fragment cono nnncnnnoncona nono 32 4 2 1 Building Structures Using Place Mode eese 34 4 2 2 Building Structures Using Grow Mode in 36 Maestro 6 5 User Manual iii Contents 4 3 Building a Structure From Atoms 2 2 a oett eo pipe rege lada 36 AA Changing Elements nero reb tene eb e eir ERREUR 38 4 5 Changing the Bond Order and Formal Charge ses 39 4 6 Fusing or Connecting Structures i 40 4 7 Adjustino the CIeor etty reete teen ia 42 4 8 Applying a Hydrogen Treatment econ iaia 43 4 9 Changing Atom Properties ia eere e ER ER Eee 45 4 10 Changing Residue Proper es eere rada 49 4 11 Desig D mimy Alo csi ec eee tere Pe
180. lectors open and to which job files are written The default initial working directory is the Maestro startup directory By changing the settings in the Directory folder of the Preferences panel you can specify a default working directory In addition to the option Maestro s current working directory you can choose from Project directory Parent of project directory Project jobs directory and Other If you choose any of the project related options the working directory is automatically updated when you begin working in a different project If you choose Other you must enter a directory in the Directory text box The Other option may be useful if you keep all Maestro related files in one area of your home directory If you change the working directory using the cd command in the command input area the selection made in the Directory folder is superseded However if the selection is project related it is reapplied if you open a new project If you use the filter in a file or project selector the filter is retained until you change it or change the working directory 12 2 5 Customizing Atom Label Appearance The Label folder of the Preferences panel contains controls for defining the separator between properties in atom labels the font and the location of the label You can also choose whether to display labels for hidden atoms and display the property name in the label as well as the property Changes made in the label preferences are im
181. lick the default Quit do not save log file button If you are working in a scratch project and you have not saved the project you will be prompted to do so Maestro 6 5 User Manual 15 Chapter 2 Maestro Overview Quit quit ex If you want to save a file that Log file name maestrolog cmd records the operation sequence for this Maestro session enter a name for the file here and then click Quit save log file Quit save log file Click Cancel to close the panel Quit do not save log file and abort the Quit operation Cancel Help Figure 2 3 The Quit Panel 16 Maestro 6 5 User Manual Chapter 3 Importing and Exporting Structures and Data The primary place for reading and writing data from Maestro is a project When you open a project the structures and data from that project are read into Maestro As you modify structures and data they are automatically saved in the project unless you have selected an option not to do so Projects are described in detail in Chapter 8 In addition to reading and writing to projects Maestro can also read and write structural information in a variety of formats including its own native Maestro format MacroModel PDB Sybyl Mol2 and MDL SD format Through the Jaguar panel structural information can be obtained from the input and output files of a wide variety of quantum chemical programs Obtaining structures from a file in Maestro is called importing rather than read
182. lot entry properties Import structures Open the Import panel to import structures into the project Export structures Open the Export panel to export structures to a file FREE Maestro 6 5 User Manual 81 Chapter 8 Projects 4 X 144 14 d dd rx EL al Columns menu Display a menu for adjusting the column widths Entry selection Open the Entry Selection dialog box to select entries based on criteria for entry proper ties Go to start Display the first selected structure Previous Display the previous structure in the list of selected structures Play backward Display the selected structures in sequence moving toward the first Stop Stop the ePlayer Play forward Display the selected structures in sequence moving toward the last Next Display the next structure in the list of selected structures Go to end Display the last selected structure ePlayer loop menu Display a menu of options for repeating the display of the structures Single direction displays structures in a single direction then repeats Oscillate reverses direction each time the beginning or end of the list is reached 8 3 2 The Project Table Menus The menus on the Project Table menu bar are described briefly below The use of the menu items is discussed later in this chapter The Table menu Provides tools for finding text sorting entries and plotting properties for importing and exporting structures and for conf
183. lows you to record notes about the project To record notes choose Annotation from the Project menu The Project Annotation panel is displayed You can enter new text or modify existing text in the text box The date and time of project creation and each annotation is recorded by default but this informa tion can be modified or deleted 8 2 Adding Entries to a Project Projects are made up of entries Entries can contain multiple structures and their proper ties Each entry has both a name by which it is identified internally and which can be modified by Maestro and a title which can be set or changed by the user but is otherwise not modified by Maestro You can add entries to a project by importing structures from a file by creating entries from structures you have built in the Workspace or by merging entries from a different project In addition you can create new entries by splitting or duplicating an existing entry or by incorporating the results of a job into the Project Table 8 2 1 Importing Structures From a File When Maestro imports structures from a file the structures are copied translated into entries and incorporated into the current project Structures can be imported from Maestro MacroModel PDB Mol2 SD and other files using the Import panel Multiple molecular structures can be imported simultaneously from multiple files and you can choose which structures if any are included in the Workspace upon import Entry
184. lp Figure 12 13 The Command Aliases panel 150 Maestro 6 5 User Manual Chapter 12 Customizing Maestro 12 5 Customization Using Command Scripts Some Maestro interface customization options can be set for the present session but are not automatically retained for future sessions To use these settings each time you launch a new Maestro session you can create a startup script that will make the settings for you To create a startup script use the controls on the Command Script Editor panel and then save the script in your preferences directory under the file name maestro cmd Each time you subsequently launch Maestro this script is used to override the system wide startup settings with your personal preferences To open the Command Script Editor panel choose Command Script Editor from the Edit menu 12 5 1 Command History By default most of the internal Maestro commands generated when you perform actions are logged in the Command History list in the Command Script Editor panel This written record of your commands is provided mainly to make the scripting process simpler Since you can perform an operation then cut and paste the resulting command into the Script list and save the script it is not necessary to memorize the Maestro Command Language Command Script Editor script Command History nic Methyl nic Carbonyl Select All Deselect All Show Hide Copy Selection To Script W Log commands Scrip
185. ls with file selection tools at the top and action buttons at the bottom Selecting a directory To select a directory you can enter it in the Path text box navigate to it in the Directories list or click Launch Directory or Current Directory to select the 26 Maestro 6 5 User Manual Chapter 3 Importing and Exporting Structures and Data directory from which you launched Maestro or the current working directory The path and the directory and file lists are updated for the chosen directory Selecting a file If the file exists you can select it in the Files list or enter its name in the File text box If you want to export to a new file enter the name in the File text box You can specify an absolute or relative path in the File text box in addition to the file name Existing files will be overwritten Selecting entries to export data from The Entries option menu allows you to choose different classes of entries to export data from All Shown Selected and Included For more information on showing selecting and including entries see Section 8 4 on page 85 and Section 8 5 on page 89 Selecting properties to export You can choose to export all properties or only the shown properties using the Properties option menu The row number and the inclusion state are not exported but all other properties are The entry name is always in the first column Selecting a delimiter You can choose from the two standard delimiters a comma and a
186. ly add it to the project However you can use a scratch entry as input for some jobs and the results can be incorporated More information on projects is given in Chapter 8 2 6 Job Launching and Incorporation Maestro s job launching and incorporation capabilities are designed to make it easy to manage multiple structures and their passage though multiple computational programs without having to deal with the details of the file system For all computational programs the Monitor panel is automatically displayed when the job is launched and job progress is posted to the monitor window You may cease or resume monitoring at any time and you can monitor any currently running job If a job finishes while it is being monitored its output is incorporated into the current project immediately If you choose to monitor an already completed but not yet incorporated job the output of that job is incorporated For more information on job control and incorporation see Chapter 14 LigPrep MacroModel and QikProp These computational programs which have been fully integrated with the Project Facility can use Maestro structure files single or multiple project entries and structures displayed in the Workspace as input and can incorporate job results into the project You can specify whether the output structures will be appended to the project replace the input entries or 12 Maestro 6 5 User Manual Chapter 2 Maestro Overview be ignore
187. mber i m formal charg i m representation i m visibility S m atom name Appendix A The Maestro File Format The atomic number The formal charge The representation used to draw this atom A flag to indicate whether this atom is displayed in Maestro or not The user specified atom name The separator for the end of the data items Next follow the data values The first column contains an index number that is assigned automati cally Remaining columns represent the data values in the same order as data names given above 1 3 0 547623 1 262401 0 990300 JN e 2 0 00000 0 00000 CHEX m i 6 0 0 1 ui 2 3 0 930177 1 296701 1 411700 qM oe 2 0 00000 0 00000 CHEX EL 6 0 0 1 TN 3 3 1 821477 1 772701 0 253300 oct Xo oto 2 0 00000 0 00000 CHEX mot c eb 6 0 0 1 n 4 3 1 624777 0 890901 0 990300 qo dex Mn 2 0 00000 0 00000 CHEX px B 6 0 0 1 m 17 41 0 493223 0 677999 0 001900 1 x 21 0 00000 0 00000 CHEX uc 1 0 0 1 br 18 41 1 817023 0 395501 0 566000 Lt mexer 21 0 50000 0 0 00000 CHEX n2 1 0 0 1 b m bond 36 i m from im to i m order i m from rep i m to rep Maestro 6 5 User Manual The separator for the end of the data values The end of the atoms block The bond block There are 36 bonds The atom the bond is from The atom the bond is to The bond order The graphical representation for the from half bond The graphical representation for the to half bond The e
188. mediately applied to existing labels Maestro 6 5 User Manual 141 Chapter 12 Customizing Maestro Preferences prefer ETE Delete Markers Font size Project Directory Label Mouse File suffi Builder X offset 0 05 Y offset 0 15 Label font Arial Bold Small Field separator J Show label when atom hides Display headings in labels Figure 12 5 The Label folder of the Preferences panel e X Offset and Y Offset To reposition labels enter new values in these text boxes The offsets define the location of the lower left corner of the label relative to the atom position Label Font To change the font choose a font style from this option menu Field Separator By default the atom label fields are separated by a space To add a separator such as a colon semicolon or vertical bar type the character in this text box Show label when atom hides You can display labels for atoms that are hidden by selecting this option Labels for hidden undisplayed atoms are shown in the Work space but do not appear to be associated with an atom Undisplaying atoms is not the same as excluding entries from the Workspace Labels like ribbons can only be shown for included atoms however these atoms need not be displayed Display headings in labels If you select this option the label includes the descrip tions of the label fields For example if you selected Molecule Number the label is mo Inum
189. mid five coordinate 161 GK Octahedral four coordinate 162 GL Octahedral five coordinate 163 GM Octahedral six coordinate 164 GN Pentagonal bipyramid seven coordinate 165 GO Twisted cube eight coordinate 166 GP Nine coordinate 167 GQ Ten coordinate 168 GR Eleven coordinate 169 GS Icosahedron twelve coordinate 170 GT Thirteen coordinate 171 GU Fourteen coordinate 172 GV Fifteen coordinate 173 GW Sixteen coordinate 196 Maestro 6 5 User Manual Appendix C Entry Suffixes The entry names within a project must be unique Maestro uses various suffixes to ensure that the names are unique Numbers are added after the suffix to make the name unique Maestro adds a suffix when certain operations are performed on entries These suffixes are listed in Table C 1 Table C 1 Entry name suffixes Operation Suffix When Added merge projects mrg name conflict import imp always Job incorporation inc always create from Workspace wse name conflict rename entry re name conflict or multiple entries selected combine entries com name conflict disassociate dis always duplicate dup always Maestro 6 5 User Manual 197 Appendix C Entry Suffixes 198 Maestro 6 5 User Manual Appendix D Utilities Schr dinger software is distributed with a number of utility programs and scripts that can be used in conjunction with any of the computational programs These utility programs are installed in SSCHRODINGER util
190. n 68 atom selection by property laici 55 by proximity iene 56 examples sci 58 picking een 53 Atom Selection dialog box 55 atom types MacroModel A E 45 table nina di 192 united option for use 144 atoms active changing i 37 changing element n 38 coloring liinda 59 coloring with schemes 61 deleting iii 51 AA esposo 50 107 Maestro 6 5 User Manual hydrogen adding 43 labiales 67 molecular representation 61 MOVIDOS ciccia 32 37 NAMES M 47 A rises tiii cripta 38 selecting for measurements 104 valency violation ss 37 Auto Help facility axis display in plots B Babel structure file format conversion PIOSTAlN A tarte 19 22 25 Ball amp Stick representation APP iii tadas 61 A dns 64 Balloon help ettet 181 bond order CHAN SINE cen teme e or eri 39 increasing in Draw mode 31 representation in 63 template for pdbconvert 202 bonds changing order Of 39 displaying order Of 63 hydrogen displaying 105 representation iene 62 smoothing of lines ss 63 Build panel uem itt 31 Atom Properties folder 38
191. n Translation Scope section is selected In order to see the atoms you want to pick for a local transformation it may be necessary to rotate the structure If this is the case select Global in the Rotation Translation Scope section rotate the structure then reselect Local to define atoms for local transformation If you want to translate atoms you need not define a center for transformation Once you have selected the atoms for transformation you can perform the desired translation 7 2 2 Selecting a Rotation Center To perform local rotations a center for rotation must be defined By default Maestro selects the centroid of the atoms selected for transformation as the rotation center If Show Markers is selected the rotation center is displayed in the Workspace as a purple ball If the assigned centroid is not satisfactory select a new center using the tools in the A Center For Transformation section Displaying atom number labels may be helpful for deter mining which atom you would like to specify as the rotation center 7 3 Tiling Multiple Entries To arrange multiple included entries into a grid pattern in the Workspace click the Tile Entries button in the toolbar ojo This operation changes the coordinates of the structures in the entries The entries are arranged according to the order they appear in the Project Table To reverse this operation choose Undo action from the Edit menu or click the Undo Redo button in the tool
192. n a table cell Include an entry exclude all others Move selected entries Paste text into a table cell Resize rows or columns Select an entry deselect all others Select or include multiple entries Toggle the entry selection or inclusion state Click repeatedly in a cell to cycle through the possible values On Off Clear Right click anywhere in the entry If the entry is not selected it becomes the selected entry The chosen action is applied to all selected entries Right click in the column header Click in the cell and edit the text or value Click the In column of the entry Drag the entries Middle click Drag the boundary with the middle mouse button For an unselected entry click anywhere in the row except the In column for a selected entry click the row number Click the first entry then shift click the last entry Control click the entry or the In column Maestro 6 5 User Manual 83 Chapter 8 Projects 8 3 4 Project Table Shortcut Keys Some frequently used operations have been assigned shortcut key combinations The shortcuts their functions and their menu equivalents are listed in Table 8 2 Table 8 2 Shortcut keys in the project facility Keys Action Menu Equivalent ALT A Select all entries Select gt All ALT F Fix entry in Workspace Entry gt Fix ALTH I Show import panel Table gt Import Structures ALT N Include only selected entries Entry gt Include Only
193. n also increase the bond order in Draw mode by drawing another bond between the two atoms To decrease the bond order click the Decrement bond order toolbar button CC then click the bonds whose order you want to decrease Each click decrements the bond order by one to a minimum of 0 Zero order bonds are displayed with a green line When you change the bond order the valence states of the atoms can be violated Maestro gives no warning of this violation so it is up to you to ensure that your structure is valid To increase the formal charge click the Increment formal charge toolbar button Y then click the atoms whose formal charge you want to increase You can only increase the formal charge one atom at a time However the formal charge is also set when you change the MacroModel atom type To decrease the formal charge click the Decrement formal charge toolbar button then click the atoms whose formal charge you want to decrease Like increasing the formal charge you can only decrease the formal charge one atom at a time and the formal charge is set when you change the MacroModel atom type Maestro 6 5 User Manual 39 Chapter 4 Building Structures 4 6 Fusing or Connecting Structures To build some structures it is sometimes convenient to connect or to fuse two existing structures Connecting two structures creates a new bond between two selected atoms with deletion of appropriate hydrogens An example is the creation of
194. n atom labels Method Linear a 0 34 1 00 ECC ET Linear start Linear end 1 50 Density Alignment depth W Adjust clipping to preserve depth cues Enhance Depth Cues Figure 12 12 The Fog folder of the Display Options panel Fog options are preserved between Maestro sessions 12 3 6 Depth Cues When you are viewing in stereo or in perspective and you zoom in on a structure the structure can appear to flatten This happens because the entire depth of the structure remains in the field of view when you zoom in it is not clipped at all and the depth cues eye separation or perspective scale are not preserved You can preserve depth cues by selecting the Adjust Clipping to Preserve Depth Cues option When you do this the front part of the structure is clipped as you zoom in so that you see only the parts of the struc ture that are in front of you not the parts that are behind you The depth cues are affected by the location of the clipping planes the closer they are to the structure the better the depth cues To move the clipping planes in to the fit the parts of the structure currently displayed in the Workspace click Enhance Depth Cues in the 3D folder or click the Enhance depth cues button in the toolbar o Maestro 6 5 User Manual 149 Chapter 12 Customizing Maestro 12 4 Creating Command Aliases If you choose to use command scripts to perform operations in Maestro you may find that th
195. n be used to display any combination of predefined information or user specified text For instance you might want to display atom numbers so that you can retype a specific atom or to pick atom pairs for superposition inclusion in a set or measurement Atom labels are persistent The labels are stored as part of the entry and are restored when an entry is excluded from then included in the Workspace However labels that are depen dent on the numbering in the Workspace such as Molecule Number may change because they are relative to the Workspace not the entry Maestro 6 5 User Manual 67 Chapter 6 Displaying Structures Atom Labels labelatom Mode add vy Remove Update Existing Label paate Existing Labels Label atoms Clear All Labels W Pick Atoms a Al select Composition Color Hetatom Labels W Element L PDB atom name L Residue name Atomic number Atom name Residue number E Atom number O Atom type MacroModel Chain name LI Grow name Atom by molecule _ Molecule number Atom by entry C Formal charge J Molecule s by entry J R S chirality Partial charge a Title L E Z stereochemistry H Solvation charge Entry name S User text Figure 6 8 The Atom Labels panel To open the Atom Labels panel choose Atoms Labels from the Display menu Options for labeling atoms with a variety of atom molecule
196. n in a scratch directory by default rather than in the directory from which the job was started When a scratch directory is used output and log files are created there and are copied back to the output directory when the job finishes or when the job is being monitored in Maestro When a scratch directory is created automatically it is named tmpdir username unique_name The unique_name is usually the job name but it can also have a sequence number appended to it in order to make the directory name unique There are a number of ways to specify the tmpdir directory The job control facility uses the first specification found from the following list e The directory given on the command line with the TMPDIR option For example SCHRODINGER bmin TMPDIR scr mmod_tmp job name Maestro 6 5 User Manual 161 Chapter 14 Job Control The directory specified by the SCHRODINGER_TMPDIR environment variable if this is set on the machine on which the job is started To set this environment variable execute the following command or add it to your shell startup script csh tesh setenv SCHRODINGER_TMPDIR scratch directory bash ksh export SCHRODINGER_TMPDIR scratch directory The directory specified by the tmpdir setting for the host entry in the host database file schrodinger hosts For remote jobs the following locations are also considered if none of the above specifi cations is found The directory speci
197. n the file selector locate and select the desired plt or vis file Then in the Choose Entry dialog choose the entry to which the surface or volume data will belong Once you have associated the data it becomes a part of the Maestro project It can be displayed by clicking the V button in the Surf column of the Project Table or by using the Surface Table panel Jaguar plt files always contain volume data 3D grids with data values at each point They may contain orbital electron density spin density or electrostatic potential informa tion These files are created using a plot section or the appropriate keywords in the gen section in the Jaguar input file A Maestro vis file contains volumes surfaces or both A volume contains all of the data values for each of the points on the grid Once the file is imported into Maestro one or more surfaces can be created In addition if the vis file still contains the original volume data used to generate an imported surface you can change the isovalue in Maestro and generate new surfaces using different isovalues If a Maestro vis file contains only surfaces then it contains only a description of the surface and not the original volume data from which it came You cannot change the isovalue for such a surface in Maestro You can create plt or vis files using the Jaguar panel When you run a plot job from the Jaguar panel the surface and volume data is automatically incorporated into the projec
198. names and titles are automatically assigned if they do not exist and are read if they do exist See Chapter 3 for more information on importing structures 78 Maestro 6 5 User Manual Chapter 8 Projects 8 2 2 Creating Entries From Workspace Structures When you build structures in the Workspace from scratch these structures constitute a scratch entry and are not saved in the project To save the scratch entry in the current project choose Create Entry From Workspace from the Project menu and type an entry name in the dialog box that is displayed If you choose an existing entry name Maestro appends wsen to the entry name to ensure that the name is unique where n is a number starting from 1 All structures in the Workspace are placed in the entry that you create You can also create an entry using the Create entry from Workspace button in the toolbar 8 2 3 Incorporating Entries From Job Output When you use selected or included entries from a project as input for a MacroModel Basic Impact QSite or QikProp job you have the option to incorporate the job results as entries in the Project Table You can choose to append the new entries to replace the input entries with the new entries or you can choose to ignore the output and not incorporate them into the table at all When you use entries for a Jaguar job the results are automati cally incorporated by appending new entries Incorporated entries have incn appended to the entry name
199. nd of the data names for bond data 189 Appendix A The Maestro File Format What follows are the data items for the bond block The first column contains an automatically assigned index number for each item 190 1 2 35 36 2 Loto L 1 The end of the bond data items The end of the bond block The end of the CT block Maestro 6 5 User Manual Appendix B Atom Types Maestro atom types are not hard wired into the program but are read in at run time from a file called atom typ We continue to use the original MacroModel atom types for most applications but now have a mechanism for easily adding new types The list of explicitly supported atom types has been expanded to include Lit Na K Rb Cs Ca Ba Mg Mn Mn Mn Mn Mn Mn Fe Fe Co Co Ni Ni Cut Cu Zn Mo Mo Mo Mo and CT You can add your own atom types and supply parameters for these types in the force field file The default atom typ file is the one located in SCHRODINGER mmshare vversion data A local file of this name overrides the default as does a local file whose name is file name typ where filename is the stem of the filename mae file This system of default version with local overrides is analogous to that used for force field and solvation files Currently Maestro accepts atom types up through number 300 We restrict the type numbers that we supply to the range
200. nformation on selecting atoms see Chapter 5 4 1 The Build Panel The Build panel consists of a toolbar and three tabbed folders The primary building tools are contained in the Fragments folder and the toolbar The Fragments folder contains several fragment libraries from which you can select a fragment and add it to the Work space either by positioning it manually or by using predefined grow rules The other two folders Atom Properties and Residue Properties contain tools for changing the properties of atoms or residues To open the Build panel choose Build from the Edit menu or click the Show Hide Build panel button on the main toolbar Pas The Fragments folder is displayed by default The toolbar of the Build panel provides quick access to tools for drawing and modifying structures and labeling atoms See Section 2 3 1 on page 7 for a description of the types of toolbar buttons The toolbar buttons are described below and their use is described later Draw VA Draw structures freehand in the Workspace Menu button with a list of elements to draw a with default C Each click in the Workspace places an atom and connects it to the previ ous atom Delete A Choose an object to delete Menu button with a pick menu and other items Same as the Delete button on the main toolbar I Set element Pick atoms to change to the selected element default C Menu button with a list of target elements Menu button with a limited list
201. ng also changes the atom coordinates The coordinate system in Maestro is oriented so that the positive z axis points out of the screen the x axis is the horizontal axis and the y axis is the vertical axis 7 1 Global Transformations Global transformations are defined as rotation and translation of the entire structure or set of structures in the Workspace The axes for rotation and translation are assigned to combinations of mouse buttons with the SHIFT and CTRL keys These assignments are given in Table 7 1 Global transformations do not actually change the coordinates of the structures in the Workspace Rather they change the view of the structures You can save and restore a particular view of the structures from the toolbar see Section 2 7 2 on page 15 for details However if you want to change the coordinates of the structures to reflect the new view you can do so by choosing Update Coordinates from the Build menu To perform a global transformation position the cursor in the Workspace and hold down the relevant key and mouse buttons while you move the mouse You should take care that you do not click instead of drag because clicking might have a particular action associated with it in the context in which you are working and change the structure To select a new center that defines the axes for rotation you can spot center the molecule on an atom by right clicking on the atom The other operation that does not change the coo
202. ng or removing atoms from the display The latter include global transformations translation rotation and magnification zoom These operations do not change the coordinates recorded in the project entry but store a local copy that is translated rotated or magnified 2 7 Undoing Operations on the Structures Single operations in the Workspace can be undone by choosing Undo action from the Edit menu This item is dynamic its name includes a description of the undoable actions and changes to Redo after it has been used Selecting Redo action reimplements the action that was undone This menu item is mapped to the Undo Redo button on the toolbar To undo the last operation do one of the following e Click the Undo Redo button on the toolbar fe Choose Undo action from the Edit menu Type ALT Z If you want to be able to undo more than one operation you can define an Undo Block The Undo Block groups a sequence of commands so that the effect of the entire sequence can be reversed This is particularly useful for risky or complicated procedures To define an Undo block 1 Choose Begin Undo Block from the Edit menu 2 Perform the sequence of operations that you want to be able to undo 3 Choose End Undo Block from the Edit menu To undo the operations in an Undo block Choose Undo action from the Edit menu type ALT Z or click the Undo Redo button in the toolbar As for a single action the Undo option for a block
203. nose form The natural state Of most sugars is the pyranose form but some derivatives assume a furanose form Maestro provides both options in both D and L forms Metal centers and ligands These libraries contain common ligands used in inor ganic chemistry and metal centers with various coordination numbers but with the specific metal undefined To change the metal type retype the center once it is placed in the Workspace using the Elements menu option in the Atom Properties folder Amino acids The Amino acids library contains the 22 naturally occurring amino acids The Nonstandard amino acids library includes the D forms of the 22 naturally occurring amino acids and various other residues Nucleic acids The Deoxyribonucleic acids library contains Adenosine Cytosine Guanine and Thymine while the Ribonucleic acids library contains Adenosine Cytosine Guanine and Uracil Protein capping groups This library contains some common molecules used to cap peptides To select a fragment library choose the library from the Fragments option menu The area below this menu contains a grid of buttons that you use to select fragments Each button displays either the name of the fragment an abbreviation for the fragment name or the fragment structure If a structure is displayed the name of the fragment is given in the Balloon help for the button Maestro 6 5 User Manual 33 Chapter 4 Building Structures Build build i ex AX
204. ns open the Command Script Editor panel ensure that Log Commands is selected and that all commands are shown If you already have a maestro cmd file in your preferences directory and you want to save the commands in this file open it in the Command Script Editor panel before you perform the new customizations If you no longer want to override the system wide settings with your personal startup preferences delete your maestro cmd file or move it out of this directory Maestro 6 5 User Manual 153 Chapter 12 Customizing Maestro After performing each customization select the relevant commands in the Command Script Editor panel and copy the resulting commands into the Script text area When you have completed all customizations save the script To set the Workspace background color 1 Choose Display Options from the Display menu of the main menu bar 2 Click the Background tab 3 Choose a color in the By Palette folder or select a color name in the By Name folder To specify a stereo viewing method a Choose Display Options from the Display menu of the main menu bar 2 In the 3D folder click the Stereo tab 3 Choose a stereo display technique from the Method option menu 4 Adjust the Size Factor and Scale Factor if necessary To enable perspective 1 Choose Display Options from the Display menu of the main menu bar 2 In the 3D folder click the Perspective tab 3 Adjust the Perspective Scale if needed
205. nsitive help that appears when the cursor is allowed to rest on an object The balloon disappears when you move Maestro 6 5 User Manual 181 Chapter 15 Help the mouse You can temporarily disable Balloon help using the Show Balloon Help item on the Help menu Balloon help is not available for all interface components 15 3 Manuals and Release Notes If you have difficulty installing Maestro see the Schr dinger Product Installation Guide If you have questions about a computational program that you have purchased see the User Manual or Reference Manual for that program Manuals are available in printed form and in PDF format on the program CD and the Schr dinger web site Each product is accompanied by a Release Notes document This document contains information about new features bugs fixed issues and workarounds If you encounter a problem with the software check the release notes for known problems 15 4 The Schr dinger Web Site The Schr dinger web site http www schrodinger com contains information about all our products In the Support pages you can find the manuals in PDF format http www schrodinger com Support pdf html and a list of frequently asked questions http www schrodinger com Support fags html for each of the products The manuals on the web site are the most up to date The manuals page contains links to corrections and addi tions to the documentation The web site also contains information about prod
206. o apply the treatment to selected atoms use the picking tools in the Modify Hydrogen Treatment section or click Select to open the Atom Selection dialog box and define the selected atoms If the structure already complies with the treatment you selected no changes will be made when you click Apply Current Treatment To All Atoms You can also apply the current hydrogen treatment to selected atoms molecules residues chains or entries from the main toolbar or the Build panel toolbar Select one of these enti ties from the Add hydrogens button menu H then click on atoms in the Workspace to apply the treatment Double click this button to apply the treatment to all atoms in the Workspace Each time you select a force field in the Potential section of a MacroModel or Impact energy panel the hydrogen treatment is automatically changed to comply with that force field and the hydrogen treatment for any atoms you subsequently draw in the Workspace will have the new hydrogen treatment If you attempt to start a MacroModel Impact or Jaguar job using an input structure with an incompatible hydrogen treatment the job fails 44 Maestro 6 5 User Manual Chapter 4 Building Structures 4 9 Changing Atom Properties In addition to changing the element and the formal charge you can change a variety of other atom and residue properties The tools for making changes are in the Atom Proper ties folder Each choice of property from the Property menu
207. o be set on this host when any job is started The syntax of the setting is variable value where variable is the environ ment variable and value is its value For example env SCHRODINGER_THIRDPARTY software databases To set multiple environment variables include one env setting for each variable 14 1 4 Software Version Selection When a job is started on a local host the job control facility compiles a list of software versions that are available on the host and selects the first compatible version on the list The list is compiled by combining lists from the following sources in the order given 1 Software in the directory specified by SCHRODINGER 2 Software in the directory specified by the schrodinger settings in the localhost entry and the entry for the host in schrodinger hosts The list from each source is sorted by architecture and release version before it is combined with the other lists This list can be displayed by entering the command for the program with the LIST option in a terminal window If you are running a job from the 166 Maestro 6 5 User Manual Chapter 14 Job Control command line you can filter this list to select a version a release and an architecture See Section 14 5 on page 174 for more information The version that is selected is not always the most recent nor is it always the version spec ified for the host in the host entry in schrodinger hosts The way in which the list is ordere
208. obal transformations When you begin a local transformation Maestro auto matically begins an undo block As a result selecting Undo action from the Edit menu reverses all operations that occurred between the time that the mouse button was pressed and the time that it was released You can switch between global and local transformations by selecting Global or Local in the Rotation Translation Scope section of the Advanced Transformations panel by using the shortcut keys ALT G and ALT L in the Workspace or by clicking on the Global Local button on the toolbar When the button is indented local transformation is in effect While you are in local transformation mode you can switch to global transformation mode temporarily by holding down the spacebar while you perform a transformation 7 2 Selecting Atoms for Transformation To select the atoms that you want to move use the tools in the Atoms For Transformation section You can pick atoms in the Workspace click Select to select atoms using the Atom Selection dialog box or enter an ASL expression in the ASL text box You can also use the Local Transformation button menu to select an object and pick it in the Workspace Maestro 6 5 User Manual 73 Chapter 7 Manipulating Structures If Show Markers is selected the atoms are marked with yellow circles connected by yellow lines Once you have started to select the atoms in the Atoms For Transformation section the Local option in the Rotatio
209. of target elements Maestro 6 5 User Manual 31 Chapter 4 Building Structures et eC 4 2 Increment bond order Pick a bond to increase its bond order by one to a maximum of 3 Decrement bond order Pick a bond to decrease its bond order by one to a minimum of 0 Increment formal charge Pick an atom to increase its formal charge by one Decrement formal charge Pick an atom to decrease its formal charge by one Move Pick an atom to move in the xy plane or the z direction Menu button with a list of drec tions Moves in the xy plane are made by clicking the new location Moves in the z direc tion are made in 0 5 increments Label Apply heteroatom labels as you build a structure The label consists of the element name and formal charge and is applied to atoms other than C and H Display Connect Fuse panel Open the Connect amp Fuse panel so you can connect structures create bonds between structures or fuse structures replace atoms of one structure with those of another Display Adjust panel Open the Adjust panel so you can change bond lengths bond angles dihedral angles or atom chiralities By default the Dihedral folder is displayed Add hydrogens Pick to apply the current hydrogen treatment Menu button with a pick menu and an item to open the Atom Selection dialog box Same as the Add hydrogens button on the main toolbar Building a Structure From Fragments Whenever possible you should use fragments
210. oint with any combination of the corresponding entry name the x axis property value and the y axis property value To remove data point labels click Unlabel Points then click on the labeled point 116 Maestro 6 5 User Manual Chapter 10 Plotting Label Points J Entry name _ X axis property _ Y axis property Label Cancel Figure 10 3 The Label Points dialog box 10 2 4 Selecting and Deselecting Project Entries If you click the Select entry button shown below clicking on a data point in the selected plot selects or unselects the corresponding entry in the Project Table The usual rules for selection apply to selecting data points clicking on its own includes one entry and excludes all others shift clicking includes an entry with the other included entries and control clicking includes or excludes the entry You can also select multiple data points and their corresponding entries by dragging All the data points in the bounding box have their entries selected or unselected in the Project Table k 10 2 5 Including and Excluding Project Entries If you click the Include entry button shown below clicking on a data point includes the corresponding entry in the Workspace The usual rules for selection apply to selecting data points clicking on its own includes one entry and excludes all others shift clicking includes an entry with the other included entries and control clicking includes or excludes the entry You c
211. omati cally for the synchronization mode superimposing structures changes the coordinates of the structures involved If you do not want to save the coordinates that result from using the ePlayer choose Only When Specifically Requested for the synchronization mode In Continuous mode coordinate changes that result from superposition are saved to the project only if you have selected Save workspace at each step in the General section Run script at each step In addition to superimposing structures you can execute a command script when each structure is displayed If you choose Current Script the script that is currently loaded in the Command Script Editor panel is executed for each structure You can open this panel and edit the script by clicking Edit If you choose From File you can choose the file that contains the command script you want to execute This script is not loaded into the Command Script Editor panel but is stored temporarily 8 7 Entry Properties Maestro supports incorporation and display of properties and calculated data for project entries You can display delete sort and filter entries based on property values You can select a subset of properties to view and you can add delete copy and rename properties Some properties of structures can be calculated by Maestro such as the molecular weight number of residues and statistics of structural features You can export properties to and import properties from a sprea
212. onvert utility 201 error reporting in Maestro PDB conversion 21 ESL see Entry Selection Language ESL excluded entries eter 80 execution host 165 167 Export panel oe ener 24 Export Spreadsheet panel 27 Extended Radius Surface panel 126 extended radius surfaces see surfaces extracting subset of structures Maestro input file 203 SD inputs tsi fees Sian ines 204 F field names job record 172 file extensions imported files erit 18 preferences file format export selecting import selecting MacroModel conversion to from 199 Maestro 6 5 User Manual Index Maestro description 185 Maestro example cece 187 Mol2 conversion to from 200 PDB conversion to from 200 TECOPIZEd usino nia 19 SD conversion to from 202 files exporting data to sess 26 importing data from 28 importing structures from 78 JPEG writing eee 159 OVErWIIINE cicci iii 25 selecting for iIMport 18 TIFF Writing 159 writing structures to n 23 fill volume CPK representation 64 Find panel nanna lara fixed entries format conversion see converting file formats formats
213. oolean operators click Boolean The Sets Boolean panel is displayed On the upper left and right sides of this panel are two columns listing every existing set Between these two panel are buttons for four boolean operators AND OR XOR and NOT The AND operation includes atoms that are common to the two sets The OR operation includes atoms that are in either set The XOR operation includes atoms that are in either set but not in both The NOT operation includes atoms not in the first set To create a new set using one of the first three operations select a set in each column and an operation To use the NOT operation select a set from the first column and select NOT After you have made your selection enter a name in the New set name text box and click Create 110 Maestro 6 5 User Manual Chapter 9 Tools Sets Boolean BG Q OR Y XOR vy NOT J Use set names in the new definition Hide Help Figure 9 5 The Sets Boolean panel The new set is defined by an ASL expression that is a combination of the expressions used to define the constituent sets If you want the ASL expression to use the set names instead of the ASL defining the sets select Use set names in the new definition If you use set names the new set is dynamically defined and inherits any changes you make to the constituent sets Otherwise the new set is statically defined 9 4 4 Reading and Writing Sets Set definitions can be saved to disk and used ag
214. options can be selected from the Loop submenu of the ePlayer menu or the Loop button menu on the toolbar rx e al If you choose None the ePlayer displays the selected structures once in the direction you choose and stops If you choose Single Direction the ePlayer displays all selected structures in sequence then loops back to the first structure and redisplays the entire series until you click another ePlayer directional button If you select Oscillate the ePlayer displays all of the selected structures in the forward direction then in the reverse direction and repeats this sequence until you click another ePlayer directional button 8 6 2 ePlayer Options The ePlayer Options panel provides access to controls for the ePlayer and extra actions that can be performed during play To open the ePlayer Options panel choose Options from the ePlayer menu The panel has three sections general options options for superim posing structures and options for running a script Maestro 6 5 User Manual 93 Chapter 8 Projects General You can adjust the speed at which the ePlayer moves through the specified structures by entering a value in seconds in the Speed text box This is the time that each structure is displayed in the Workspace The default is zero seconds per entry which means that the speed of play is limited only by the speed of rendering of the structures In Continuous play mode the structures are only temporarily displa
215. orted file select Selected Entries Exporting to single or multiple files You can export entries to a single multi structure file or to multiple files that each contain a single entry From the Files option menu choose either Export All Entries To A Single File or Export Each Entry As An Individual File If you export structures using one of the Babel supported formats you can only export a single structure to each file In this case you should not choose Export All Entries To A Single File 3 2 2 Exporting Multiple Files If you want to save each entry to a separate file you must specify how to name the files by choosing one of three naming schemes from the File Names Are option menu The naming schemes are described below File Name Entry Name If you choose File Name Entry Name you must select a file or type in a file stem The entry name and the file suffix are appended to the file stem If you choose a file name the suffix is the suffix of that file name For example if you are exporting the entries combination 3 combination 4 and combination 5 in Maestro format and you select the file structure dat the new files are named structure combination 3 dat structure combination 4 dat structure combination 5 dat If you typed in the file stem HIV the following files would be written Maestro 6 5 User Manual 25 Chapter 3 Importing and Exporting Structures and Data HIV combination 3 mae HIV combination 4 mae HIV combin
216. orting Structures in 17 Included entries tts 80 AAA te eite 80 incorporation of job results 12 176 installation directory specifying for host 166 ISOSULTACO ici ii 123 Isosurface dialog box 135 isovalue 123 135 restrictions on changing 131 sitemap defaults 129 J Jaguar files importing 22 Jaguar plot files importing 131 job control configuring 161 jobcontrol utility 169 171 purging job database 173 O 169 jobs cleaning up database database incorporation options 176 214 launching introduction to 12 listiig nein nte 170 A extet feris 167 monitoring status keywords 168 output incorporation 79 176 jc siria 172 remote submission 162 175 scratch directory 161 162 Stranded iii nia 171 temporary files n 176 joining geometry specifying 36 IPEGAIES cicli 122 159 L Label Points dialog box 117 labels adding user text t0 68 Apply ME ie tere sia 69 applying while building
217. ould list the names of the hosts and user name from which the user can log in without specifying a password The list should contain two lines for each machine one with the machine name alone and one with the fully qualified name 162 Maestro 6 5 User Manual Chapter 14 Job Control machine username machine domain username The user name in the rhosts file is optional if it is the same on the remote hosts You do not need root permission to configure this file but you must make sure that the file does not have group or other write permission Once you have configured hosts equiv or rhosts use the following command to check for successful communication between the host that the job will be started on and each of the other hosts that the job will use rsh 1 username machine date This command should print the date from the host machine If you have a schrodinger hosts file you can automatically check all of the machines listed in it using the command SSCHRODINGER hunt rtest See the next section for more information about this command By default the rsh and rcp commands are used for remote connection and copying To use ssh and scp instead set the environment variables SCHRODINGER_RSH and SCHRODINGER_RCP to ssh and scp 14 1 3 The schrodinger hosts File The job control facility obtains information about the computers hosts on which it will run jobs from the schrodinger hosts file The hosts database f
218. oving the Workspace contents deselect Replace workspace To specify which structures are to be included in the workspace choose one of the options from the Include in workspace option menu No Imported Structures First Imported Struc ture or All Imported Structures The default is First Imported Structure If you choose No Imported Structures and Replace workspace is selected the Workspace is cleared Importing graphical information If you import structures from a Maestro file you can also import graphical information for the structures such as the molecular representation Maestro s default behavior is to read in and use this information when importing struc tures from a file If you do not want imported structures to be displayed using the saved representation information clear the Use graphical info option 20 Maestro 6 5 User Manual Chapter 3 Importing and Exporting Structures and Data 3 1 3 Error Reporting for PDB Files When Maestro imports structures from PDB files the color scheme it uses reflects the success or failure of the placement of bonds Maestro attempts to place bonds according to a set of standard residue templates the CONECT records of the PDB file and geometry If this placement of bonds fails the regions of the structure in which problems were identi fied are colored according to the type of error The color scheme is given in Table 3 1 Table 3 1 Coloring scheme for structures imported from PDB files
219. perty in the From list select lt Add New Property gt in the To list provide a property name in the New Property Name text box then click All Entries or Selected Entries A new property column is created and the values are copied for all entries or for the selected entries See the next section for more information on copying properties Maestro provides a selection of properties that can be calculated for the entry from the structure itself These calculations are done from the Calculate Properties panel which you open by selecting Calculate from the Property menu The available properties given in the Properties list at the top of the panel are Number of atoms e Number of residues e Number of molecules Molecular weight Molecular formula Molecular charge Secondary structure content Substructure The Secondary structure content property is actually three properties percentage of helices percentage of beta strands and percentage of random coils The Substructure property is the number of occurrences in each entry of the substructure that you provide Information on Maestro substructure notation is contained in the file SCHRODINGER services vversion doc mmsubs syntax txt For some properties there are options or settings that must be made in order to calculate the property These are available in the area below the property list To calculate the prop erty select it in the Property list select any options and
220. pic text type the string in the Search current topic for text box and press RETURN To locate the next occurrence of the string press RETURN again or click Next You can match the exact case of the search string by selecting Case sensitive 180 Maestro 6 5 User Manual Chapter 15 Help Help help Bo Search Categories Help categories Display Menu a Topics in this category double click to view Color Selector Display Options Panel Display Undisplay Atom Panel Molecular Representation Panel Stereo Viewing Topic Molecular Representation Pane Back Contents e Summary Opening the Molecular Representation Panel e Using the Molecular Representation Panel e Molecular Representation Panel Features e Related Topics Summary AA a ja Search current topic for Next LI Case sensitive Hide Help Figure 15 2 The Categories folder of the Help panel 15 2 Context Sensitive Help In addition to the Help facility Maestro has some other supporting help features They are described below Auto Help The Auto Help window is located just below the title bar of the main window The Auto Help facility provides automatic context sensitive help For example when you open the Atom Labels panel from the Display menu Auto Help prompts you to pick an atom to label Auto Help is not available for all operations Balloon Help Balloon help consists of a floating text box containing context se
221. play Adjust panel button on the Build panel toolbar The tools for adjusting bond lengths bond angles and dihedral angles are similar so the description given here is generic To define the geometric parameter that you want to adjust choose Atoms or Bonds from the Pick menu in the Define atoms for operation section and pick the atoms or bonds For a bond length you must pick two atoms or one bond for a bond angle you must pick three atoms or two bonds for a dihedral angle you must pick four atoms or one bond the bond about which the rotation is performed When you pick this bond the groups attached to the atom nearest the point you click are the ones that are moved Adjust adjust EEE Dihedral 60 0 W Allow Adjusting Define atoms for dihedral adjustment W Pick Bonds W Show markers Move 4 All attached atoms y All attached terminal atoms Only single atom Delete Delete All Figure 4 6 The Adjust panel showing the Dihedral folder 42 Maestro 6 5 User Manual Chapter 4 Building Structures The atom numbers of the selected atoms are listed in the text box at the top of the folder You can pick as many sets of atoms as you like before doing any adjustments The last atom that you pick is the target atom the atom that is moved in the adjustment process Once you have chosen the atoms you must decide which of the attached atoms to move along with the target
222. pplies the machine name The host setting is only needed if the name line does not give the machine address You might for example want to provide an alias in the name setting and define the host name in a host setting if the host name is long Another possible use of multiple entries for a single machine is to specify different settings on a machine such as different scratch directories or different software installa tions You can also use the name and host settings to specify a batch queue name and the host on which the batch system is available The host name does not need to include the full Internet address unless the host on which you plan to run the execution host is not on the same local network as the host from which you plan to submit jobs the submission host The value localhost is a special name setting that means the host from which the job was submitted In addition to this function the localhost entry sets the default values of settings for all other entries In the schrodinger hosts file example above the host entries ahost and bhost inherit the schrodinger setting from the localhost entry The user Setting If you have different user names on the submission and execution hosts you must include a user setting for the execution host in the schrodinger hosts file on the submission host The tmpdir Setting The tmpdir setting specifies a directory where scratch directories can be created such as scr or temp See Sect
223. r Maestro 6 5 User Manual 17 Chapter 3 Importing and Exporting Structures and Data Import import zonet dyall Tutorialsi Format Maestro A Filter Files mdo au et build_example mae sitemap1SHD mae Directories sitemap1SHD out A A fa 1SHD prj LigPrep Qui ckTopi cs 7 Ai ED Launch Directory working Directory Selection zone1 dyall Tutorials build_example mae All Files Import all structures W Replace workspace Start 1 W Use graphical info End Total 1 Include in workspace First Imported Structure Import Filter Figure 3 1 The Import panel 3 1 1 Selecting Files Selecting a file type Before you choose files you must specify the file type by choosing a file format from the Format menu This choice determines the file extensions to be used and thus the filter displayed in the Filter text box and the files displayed in the Files list The menu options are described below Maestro Import from Maestro structure files which have a mae extension or MacroModel input or output structure files which have dat or out extensions Properties are imported as well as structures PDB Import PDB files which have either a pdb or a ent extension Where multiple atomic coordinates exist for a single PDB entry Maestro chooses the atoms with the highest occu pancy ratio Properties are imported as well as structures 18 Maestro 6 5 User Manual
224. r An ESL expression that is used to select or filter entries in the Project Table grow bond The bond that is replaced when you add a fragment to a structure in Grow mode The grow bond is displayed as a green arrow in the Workspace importing Reading structures and their associated data from a structure file into a Maestro project or reading data from a spreadsheet file into a Maestro project inclusion Display of entries in the Workspace Multiple entries can be included in the Workspace The inclusion state included excluded or fixed is indicated in the In column of the Project Table isovalue the value of a property that defines a surface The property is a function of the three spatial coordinates and is represented as a set of points on a three dimensional grid menu button A toolbar button that has a menu which you open by holding down the left mouse button The button has a black triangle in the lower right corner option menu A drop down menu from which you can select an option Clicking the button on the menu displays the menu without having to hold down the left mouse button picking Selecting atoms in the Workspace project A collection of related data such as structures with their associated properties The project may include data that does not appear in the Project Table Project Table The table that displays the contents of a project with rows of entries and columns of properties The table is
225. r colored star You can delete atoms from the list by selecting the list item and clicking Delete Once you have picked all the atoms click Create Centroid Atom The To define another centroid click Delete All before picking atoms for the new centroid Centroids centroid BOE Atoms to define centroid Delete Delete All W Pick atoms to define centroid J W Show markers Create Centroid Atom Hide Help Figure 4 13 The Centroids panel 50 Maestro 6 5 User Manual Chapter 4 Building Structures 4 12 Deleting Atoms If you need to delete atoms from a structure you can use the Delete button menu on either the main toolbar or the Build panel toolbar X E This menu offers choices for the type of object to delete and allows you to open the Atom Selection dialog box to select atoms for deletion based on their properties When you delete atoms the terminal atoms that are attached to this atom can be deleted or the terminal atoms can be left in place Terminal atoms are atoms that are bonded only to that atom such as hydrogen or a halogen Deleting terminal atoms would not for example delete a methyl group attached to the deleted atom This action is controlled by an option that you can set in the Builder folder of the Preferences panel If you want to delete all atoms in the Workspace use the Clear Workspace button which is located on the main toolbar Maestro 6 5 User Manual 51 Chapter 4
226. r informa tion on the correspondence of treatments to force fields The applyhtreat utility is used by Maestro when a hydrogen treatment is applied in the Hydrogen Treatment folder of the Build panel See Section 4 8 on page 43 for more infor mation Note Hydrogen addition or deletion takes place only as necessary to make the structure consistent with the selected hydrogen treatment For example if the specified treat ment option calls for all atoms to have hydrogens and the structures in the input file already have hydrogens on all atoms no changes will be performed Maestro changes the default hydrogen treatment automatically if the force field is changed The new hydrogen treatment will be one of those acceptable for the newly selected force field Maestro 6 5 User Manual 207 Appendix D Utilities 208 Maestro 6 5 User Manual Glossary ASD Atom Selection dialog box ASL Atom Specification Language button menu The menu available from a toolbar menu button which you open by holding down the left mouse button entry A structure or set of structures and associated properties Entries are represented as a row in the Project Table and can be used as input for jobs ESD Entry Selection dialog box ESL Entry Specification Language exporting Writing structures and their associated data from a Maestro project to a struc ture file or writing data from a Maestro project to a spreadsheet file filte
227. rary output file could not be created There may be a permissions problem or the disk may be full Maestro 6 5 User Manual 21 Chapter 3 Importing and Exporting Structures and Data 3 1 4 Entry Naming Conventions for Imported Structures The names of entries in a project are required to be unique Maestro enforces the unique ness by adding suffixes to entry names to resolve any duplications When structures are imported from a file they are assigned entry names according to the following procedure Tf the file already contains entry names these names are read and used as the base of the entry name If the file does not contain entry names the stem of the file name the portion before the extension is used as the base of the entry names e The suffix impn is added to the base entry name where n is a number beginning at 1 and is incremented for each import operation Consequently entries imported from different files automatically have different entry names If the resulting entry name is not unique the suffix m is appended to the entry name where m is a number beginning at 1 and is incremented for each import oper ation For example if you imported three conformers of decane from a file in which each conformer had the name decane the entry names would be decane imp1 1 decane imp1 2 and decane imp1 3 The same naming mechanism is used when calculation results are incorporated into a project except that the suffix in
228. rdinates of the structure is zooming which is also performed with the mouse see Table 7 1 You can also fit the displayed size of the structure to the Workspace by clicking the Fit to screen button on the toolbar RA aW m Maestro 6 5 User Manual 71 Chapter 7 Manipulating Structures Table 7 1 Mapping of Workspace operations to mouse actions Operation Action Rotate about the x and y axes Drag with middle mouse button Rotate about the x axis only Drag vertically with SHIFT and middle mouse button Rotate about the y axis only Drag horizontally with SHIFT and middle mouse button Rotate about the z axis Drag horizontally with CTRL and middle mouse button Spot center on an atom Right click Translate in the x y plane Drag with right mouse button Translate along the y axis Drag vertically with SHIFT and right mouse button Translate along the x axis Drag horizontally with SHIFT and right mouse button Translate about the z axis Drag horizontally with CTRL and right mouse button Zoom Drag horizontally with middle and right mouse buttons or with SHIFT CTRL and middle mouse button To restore the view to the default view in which the view axes are aligned with the coordi nate axes of the structure click the Reset workspace button in the toolbar de XYI 7 2 Local Transformations A local transformation in Maestro is the movement of a user defined atom subset with respect to the other atoms in the Workspace such
229. re identical to that of the input entry Because project entries must have unique names the project facility uses automatic rules for creating unique entry names when the output entries are incorporated When an entry is incorporated the suffix incn is added to the entry name The value of n starts at 1 and is incremented for each incorporation event For instance if the input entry was ligand1 and the job output contained a single entry also named 1igand1 the output entry would be given the name ligandl inc1 Multiple consecutive entries bearing the same entry name incorporated from a single file are distinguished using a dot suffix Thus if the output of the above job contained multiple consecutive entries all named ligand1 then on import they would be renamed ligand1 imp1 1 ligand1 impl 2 etc See Appendix C for information on the suffixes used in entry naming Maestro 6 5 User Manual 177 Chapter 14 Job Control 178 Maestro 6 5 User Manual Chapter 15 Help This chapter describes the various ways in which you can obtain information on Schr dinger s products Maestro has an online help facility automatic context sensitive help Auto Help and Balloon help Manuals in PDF format are included with the product distribution and each product has an FAQ page on the Schr dinger web site 15 1 Maestro Online Help If you have any difficulty performing a particular operation within the Maestro interface look for ans
230. re surfaces associated with the entry the entry name and any properties associated with the entry The first four columns of the project table are always visible the row number the In column the entry name or the title you can exchange these two from the Table menu and the Surf column The remainder of the columns appear in the scrolling section of the table Project entries have two states that represent how they are being used the selection state and the inclusion state Selected entries are highlighted in the Project Table and are avail able for operations such as copying deleting or use as input to a computational program Selection of entries is discussed in the next section Included entries are displayed in the Workspace and are available for manipulation modification and other actions that can be performed from the Workspace The inclusion state is indicated in the In column Excluded entries entries that are not displayed in the Workspace are marked with an empty diamond Included entries are marked with a cross in the diamond Fixed entries entries whose display is not affected by the inclusion or exclusion of other entries are marked with a padlock icon Fixed entries are not frozen you can perform operations on fixed entries in the Workspace such as rotation and translation or adding or deleting atoms To undisplay a fixed entry you must exclude it from the Workspace The selection and inclusion states are stored in t
231. representation to all atoms You can choose the object to pick from the button menus o oU 6 2 2 Changing the Representation of Bonds In the Bonds folder you can choose between None Wire and Tube for the representation of bonds The None option means that only the atoms are displayed To change the bond representation for selected atoms use the picking tools or the Select button in the Apply current representation to atoms section Click All to apply the representation to all bonds You can mix representations within a single molecule by picking 62 Maestro 6 5 User Manual Chapter 6 Displaying Structures Molecular Representation rep BEE Settings Atoms Bonds Ribbons Representation gt None 4 Wire Tube Wire Settings Style Split Blend Represent bond orders with 4 Multiple lines Thickness Show bond orders 4 Automatically Q Always lt Never W Smoothing Apply current representation to bonds W Pick Bonds All Select Figure 6 4 The Bonds folder of the Molecular Representation panel If you choose the Wire representation several other options are also available in the Wire Settings section Style You can select Split to display distinctly colored half bonds or Blend to dis play bonds as color gradients Selecting Blend can improve graphics performance Represent bond orders with You can choose Multiple Lines to display multiple bonds as m
232. residue chain and entry properties are provided in the Composition folder of the Atom Labels panel To compose a label select as many properties as you like The properties are separated by spaces in the label If you select User Text you can enter text in the text box to include your own infor mation in the labels The color of the labels is the color of the labeled atom by default To use a fixed color for the label deselect Color label by atom in the Color folder and select a color in the By Palette or By Name subfolder These subfolders are identical to those in the Atom Coloring panel Instead of choosing your own labels you can choose from two fixed labeling schemes that label non carbon atoms with the element name In the Hetatom Labels folder you can select Labels on hetero and hydrogen atoms to label all non carbon atoms with the element label or Labels on hetero atoms to label all atoms other than carbon and hydrogen with the element label When you select either of these schemes the labels are applied immediately to all relevant atoms The Labels on hetero atoms scheme is also available from the Build panel toolbar and is applied as atoms are added to the Workspace 68 Maestro 6 5 User Manual Chapter 6 Displaying Structures To select the atoms for labeling use the tools in the Label atoms section You can use the picking tools click All to label all atoms or click Select and use the Atom Selection dialog box to choose
233. ring when the structure is not being moved 64 Maestro 6 5 User Manual Chapter 6 Displaying Structures Molecular Representation rep EEE Settings Atoms Bonds Ribbons Default representation Wire a Set all to Wire CPK Tube Ball amp Stick Rendering Wire width pixels CPK percentage Tube radius A Ball percentage Stick radius A Moving resolution Resting resolution Restore Defaults Figure 6 5 The Settings folder of the Molecular Representation panel 6 2 4 Rendering Proteins as Ribbons The controls in the Ribbons folder enable you to display protein backbones as a ribbon diagram Displaying ribbons can simplify the analysis of the protein s secondary and tertiary structures You can choose from seven ribbon styles and nine color schemes and apply the ribbon style by picking or using the Atom Selection dialog box You can mix representations within a single protein by picking You can open the Molecular Representation panel with the Ribbons tab displayed by choosing Ribbons from the Display menu on the main menu bar Ribbons are defined by a style and a color scheme The choices of style are Cartoon display loops as thin tubes sheets as arrows and helices as ribbons Ribbon thin curved flat surface that follows the backbone e Tube curved tube that follows the backbone Thin Tube thin curved tube that follows the backbone e Curved Line
234. roject facility at all Liaison takes input from specified disk files or the Workspace and the results are not incorporated QSite and Impact are integrated into the Project Facility Either the Workspace or a single selected entry can be used as the source of job input and the incorporation mode can be selected Protein preparation uses the Workspace structure as input and the resulting structures are incorporated For the programs that do not incorporate results the output files are placed in the file 1 0 directory that you specify using the Preferences panel Prime Prime s Protein Structure Prediction works on a different model from other products The input is a sequence rather than a structure though the sequence can be taken from a struc ture in the Workspace Output from each step is incorporated into the next step but not via the Project Table At the final step the structures can be copied into the Project Table The standalone Refinement facility is similar to MacroModel and QikProp it takes the struc ture in the Workspace as input and incorporates the results into the Project Table according to the selected option Maestro 6 5 User Manual 13 Chapter 2 Maestro Overview 2 7 Undoing Workspace Operations There are two classes of operations in the Workspace operations that act on the structure and operations that act on the view of the molecule The former include local transforma tions other coordinate changes and addi
235. s Toolbar Atoms 1716 1716 Entries 1 2 Res 106 Chn 3 Mol Allatomi Al1Atom1 SIQAEEWYFGKITRRESERLLLNAENPRGTFLYRESEAYCLSYSDFDNA AllAtomi Allatoni VEEI N Viewing volume indicator Sequence viewer Status bar Command input area Clipping plane Figure 2 1 The Maestro main window 6 Maestro 6 5 User Manual Chapter 2 Maestro Overview Clipping planes window displays a small top view of the Workspace and shows the clipping planes and viewing volume indicators Toolbar contains buttons for many common tasks and also provides tools for dis playing and manipulating structures and organizing the Workspace Status bar displays the number of atoms entries residues chains and molecules in the Workspace Sequence viewer shows the sequences for proteins displayed in the Workspace Command input area provides a place to enter Maestro commands You can show or hide any of the last five of these from the Display menu By default all of these are displayed except the clipping planes window You can show or hide the toolbar the status bar and the sequence viewer by clicking their collapse buttons E x When a distinction between components in the main window and those in other panels is needed the term main is applied to the main window components e g main toolbar 2 3 1 The Toolbar The main toolbar contains buttons for performing common tasks There are three kinds of buttons on the tool
236. s of properties to report If more than one property is given the names must be quoted e g p title MW This isthe same as p title p MW V Show the version number of this utility D 4 Structure Preparation applyhtreat Apply a hydrogen treatment add or delete hydrogens to one or more structures in a Maestro format file Syntax applyhtreat input file output file treatment name ASL expression Options Allowed treatment names All atom with Osp3 Nsp3 Lp All atom with No Lp Csp3 United atom with S Lp Csp3 United atom with No Lp All atom with S Lp C sp2 sp3 United atom with No Lp C sp2 sp3 N O S United atom with No Lp Default treatment All atom with No Lp The treatment name must be enclosed in quotes The ASL expression can be used to specify a range of atoms to which the treatment is to be applied It must also be enclosed in quotes The applyhtreat utility can be used to delete or add hydrogens to one or more struc tures in a Maestro format file consistent with the hydrogen treatment option that you provide A hydrogen treatment is a protocol that determines which atoms are to have hydrogens and or lone pairs attached Several different treatments are supplied Each of these treatments is associated with a particular molecular mechanics force field However 206 Maestro 6 5 User Manual Appendix D Utilities some treatments are suitable for several force fields SeeTable 4 1 on page 44 fo
237. s or dihedrals toolbar button To make a measurement choose Distance Angle or Dihedral from the button menu then pick the atoms in the Workspace The measurement is made and any options that are set in the Measurements panel are applied for example if Create property for selected entries is selected the property is created 9 2 2 Displaying Hydrogen Bonds and Contacts The procedures for displaying H Bonds and Contacts are similar Unlike distance angle and dihedral measurements you can display hydrogen bonds and contacts for an unlimited number of atoms and you define the desired atoms by placing them in sets Two sets can be defined at any given time and you can choose to display the hydrogen bonds or contacts between the atoms of a set or between the two separate sets Measurements measurements REE Measurements measurements Seiki Distances Angles Dihedrals H Bonds Contacts Distances Angles Dihedrals H Bonds Contacts W Display H bonds W Display contacts Maximum distance 2 50 Mark contacts Contact cutoff ratios Minimum donor angle 30 00 L Good contacts 1 30 Minimum acceptor angle 60 00 W Bad contacts 0 83 Atom set 1 W Ugly contacts 0 75 ASL mol num Atom set 1 Clear All Select ASL fmlnmt W Pick Molecules Clear All Select Atom set 2 W Pick Molecules ASL Do siga Select O Pick Molecules Create Property for Selected Entries Hide
238. s selected each pair is marked with a dashed green line For the pair that is selected in the list the green line is flanked by solid yellow lines The lines disappear once the connect or fuse operation is completed Delete Delete All 1 W Pick to define atom pairs W Show markers Connect Fuse Hide Help Figure 4 4 The Connect amp Fuse panel 40 Maestro 6 5 User Manual Chapter 4 Building Structures When fusing structures the order in which you select the atom pair is important The atom selected first replaced by the second selected atom For example when fusing an amino nitrogen and an ethyl carbon selecting the nitrogen first results in its deletion followed by attachment of the remaining atoms of the amine to the ethyl carbon Selecting the ethyl carbon first results in deletion of the carbon and retention of the nitrogen To delete an atom pair from the Connect or Fuse Atoms list and cancel the connection or fusion of those atoms select the pair in the list and then click Delete To clear the atom pair list click Delete All When you have selected all the pairs of atoms that you want to connect or fuse click the appropriate button Connect or Fuse If you are performing a connection or fusion between structures belonging to different project entries the source entries the result must belong to a single entry When you click Connect or Fuse the Choose Entry dialog box is displayed
239. s with the All button and clear the ASL expression with the Clear button If Show Markers is selected the atoms corresponding to the expression in the ASL text box are highlighted with light blue markers in the workspace 5 2 3 Selecting Atoms by Proximity Once you have made an initial selection you can select atoms based on their distance from the atoms defined by the current ASL expression the source atoms in the Proximity dialog box To open this dialog box click Proximity You can specify the distance in angstroms or in terms of the number of bonds If the boundary for inclusion intersects a molecule or a residue you can choose to include the entire molecule or residue using the Fill buttons You can either include or exclude the source atoms in the selection For example you might want to include residues within a 56 Maestro 6 5 User Manual Chapter 5 Selecting Atoms Proximity 4 Within 4 Angstroms w Beyond y Bonds Fill None y Residues gt Molecules Exclude source Update Markers OK Help Cancel Figure 5 4 The Proximity dialog box certain distance of a metal atom but not include the atom itself The Update Markers button updates the markers for the proximity selection so that you can view the selection in the workspace before accepting it 5 2 4 Editing and Storing Expressions You can undo multiple operations with repeated clicks on the Undo button The Redo button rever
240. se Show Plots from the Selection menu of the Project Table panel Plots are displayed in the main window of this panel Plots can be tiled or can be arranged either horizontally or vertically in the window You can display as many plots as you like in the Plot XY panel but with the addition of each plot all plots are reduced in size The zoom bar is the area at the right of the Plot XY panel It contains controls for zooming and panning the selected plots You can display it or hide it by selecting Plot Zoom Bar from the Settings menu 114 Maestro 6 5 User Manual Chapter 10 Plotting Plot XY plotxy mix Plot Settings 1000 00 Zoom 100 00 e 100 00 d Al aj di Y q Reset y Zoom Box Click To Center Drag To Zoom mol 0115 mol 0120 mol 0128 mol 0132 mol 0141 mol 0144 Figure 10 2 The Plot XY panel The Plot toolbar contains buttons for operations on the selected plot such as labeling and unlabeling data points selecting and deselecting entries associated with data points including and excluding entries associated with data points panning the plot and zooming in on the plot 10 2 1 Selecting Plots You can select a plot by clicking in it The selected plot is outlined with a dotted line You can select more than one plot by clicking in the first plot and shift clicking in additional plots Once you have multiple plots selected you can control click in a plot to remove it from
241. ses undo operations and can also be used multiple times These are the buttons in the dialog box not the toolbar button You can also type ASL expressions directly into the ASL text box The hand edited expressions are considered part of the last operation performed with the mouse and can be undone and redone as part of that operation but cannot be undone or redone separately The Create Set button opens a dialog box that enables you to name and store the existing ASL expression for use as a set definition The sets created in this manner are the same as sets created with the Sets panel and are listed in the Set folder You can therefore create sets from the Atom Selection dialog box and use them for atom selection later 5 2 5 Examples of Atom Selection Below are some examples of the use of the Atom Selection dialog box It is assumed that you have the Atom Selection dialog box open To apply your selection and dismiss the dialog box click OK These examples assume that the protein and the ligand are in sepa rate entries in the Workspace Maestro 6 5 User Manual 57 Chapter 5 Selecting Atoms To select all carbon atoms in the backbone of a protein I In the Atom folder select Element from the list of properties 2 Select C from the list of elements 3 Click Add to add the current selection to the ASL expression 4 5 6 Select Backbone Side Chain from the list of properties Select the Backbone option Cli
242. side of the ball contacts the van der Waals spheres the surfaces coincide Where two van der Waals spheres intersect the Connolly surface follows the surface of the solvent sphere producing fillets rather than cusps Changing the solvent sphere or probe radius affects the size and shape of the surface Reducing the grid spacing improves the accuracy of the surface but increases the calculation time To open the Molecular Surface panel choose Molecular Surface from the Surtaces submenu of the Display menu Instructions for using the settings in the Molecular Surface panel are described in Section 11 1 1 on page 123 11 1 3 Extended Radius Surfaces In the Extended Radius Surface panel you can generate a surface constructed on van der Waals spheres in a similar way to a Connolly surface In an extended radius surface the point that corresponds to the center of the probe is used to generate the surface rather than the point representing the closest contact of the probe with the surface An extended radius surface therefore shows roughly the surface that the centroid of a solvent or a ligand cannot penetrate Thus looking at bound ligands with wire bond representation the ligands would hug but not penetrate the extended radius surface Maestro 6 5 User Manual 125 Chapter 11 Surfaces Extended Radius Surface surfaceextra BRITES Name Extended Radius Surface Atoms for surface display ASL DT All Select W Pi
243. sidechains water molecules or hydrogen atoms If you want to display and undisplay project entries use the In setting in the Project Table panel See Section 8 5 1 on page 89 for more information about operating on project entries To open the Display Undisplay Atoms panel choose Display Undisplay Atoms from the Display menu The Display Undisplay Atoms panel is divided into two sections Each section contains control for the following three operations Also Display add the selected atoms to the atoms that are already displayed Undisplay do not display the selected atoms Display Only display only the selected atoms Maestro 6 5 User Manual 69 Chapter 6 Displaying Structures Display Undisplay Atoms displayatom Also display W Pick Select Undisplay O Pick Molecules Select Display only Ol Pick Molecules Also display Undisplay Display only Protein Backbone Protein Backbone Protein Backbone Protein Sidechain Protein Sidechain Protein Sidechain Water Molecules Water Molecules Water Molecules Non polar H Atoms Non polar H Atoms Non polar H Atoms Polar H Atoms Polar H Atoms Polar H Atoms Hide Help Figure 6 9 The Display Undisplay Atoms panel In the upper section you can choose the atoms for the operation using picking tools including a Pick menu an All button and the Atom Selection dialog box which is opened using the Selec
244. sion fails when copying to the In or Selected properties these properties are set to false In addition the Title property is required by Maestro so if you delete 1t Maestro creates a replacement title property The following conditions determine what happens when the destination is not one of the four special properties If the destination property does not exist it is created using the data type of the source property and the source data is copied into it If the destination property does exist and is of the same type as the source the desti nation property values are replaced If the destination property exists and is of a different type an attempt is made to con vert the data type to that of the destination If the conversion fails the destination property is deleted If it succeeds the converted data replaces the original data e If fields in the source property column are empty the corresponding fields in the des tination property column are deleted Note that the row number is not a property of the entry 98 Maestro 6 5 User Manual Chapter 8 Projects Delete Property Figure 8 11 The Delete Property dialog box 8 7 3 Renaming and Deleting Properties You can rename and delete properties other than the fixed properties Entry Name In Surf Title and Selected To rename a property you can edit the table cell directly by clicking in the cell changing the text and pressing ENTER or clicking elsewh
245. ste property values using the mouse To copy a value from the Project Table click in the cell then drag over the value you want to copy To paste the value click in the cell you want to copy the value to then middle click to paste the value into the cell The value you copy does not need to come from Maestro you can obtain it from any location Maestro 6 5 User Manual 97 Chapter 8 Projects Copy Property copyprop EIEE From a ami de Hami dine Hamine Himetab Hrotor HrtvFG Hstars Add New Property New property name Copy values for All Rows Selected Rows Hide Help Figure 8 9 The Copy Property panel You can copy values from one property to another in the Copy Property panel which you open by selecting Copy from the Property menu To copy values specify the source prop erty From and the destination property To then click All Rows or Selected Rows to copy the values The source and destination properties do not need to have the same data type The result of the copy operation depends on the characteristics of the data An entry must always have values for Entry Name In Surf and Selected These property values cannot be deleted The Surf property cannot be overwritten The Entry Name can only be replaced by a legal entry name If the name is legal but not unique 1t is made unique and a prompt to accept the modified name is displayed If the source value is missing or the conver
246. stro 6 5 User Manual 143 Chapter 12 Customizing Maestro Preferences prefer ETE Delete Markers Font size Project Directory Label Mouse File suffix Builder W Allow united atom types while building W Adjust bond length when atom type is changed W Adjust number of hydrogens following build operations W Delete terminal atoms Figure 12 8 The Builder folder of the Preferences panel 12 2 8 Setting Builder Preferences In the Builder folder you can set options to control the use of united atoms automatic adjustment of bond lengths removal of hydrogens to maintain valence during build opera tions and deletion of terminal atoms The options are persistent between Maestro sessions and are selected by default Allow United Atom Types While Building The use of united atom types can cause problems for users who do not want implicit hydrogen atoms in their structures such as Jaguar users United atom types with implicit hydrogens are assigned by default when hydrogens are deleted from heavy atoms If this option is deselected united atom types are never assigned when atoms and bonds are explicitly deleted atoms are retyped or structures are drawn freehand Instead the atom types remain unchanged or explicit radical types are assigned if they are available United atom types are used regardless of this option if a hydrogen treatment that requires united atom types is applied or when reading in a structure file such
247. t place 1 396908 0 649130 0 000000 fragment organic Amine attach 4 fragment organic Methyl attach fragment organic Methyl attach fragment organic Carbonyl attach 11 undo E i Run Script Sia Expand Command Aliases Open Local Open Global Save As Hide Help Figure 12 14 The Command Script Editor panel Maestro 6 5 User Manual 151 Chapter 12 Customizing Maestro Show Hide Commands a x Choose sets of keywords to be made visible or hidden Maestro Project Edit Display Monitor Application Analysis Help Side Bar others W Print print W Save Panel Layout savelayout W Preferences prefer W Command Alias alias W System system W Quit quit W Save Image saveimage Rebuild Command History Show All Commands Hide All Commands Hide Help Figure 12 15 The Show Hide Commands panel You can control which types of commands are displayed by using the Show Hide Commands panel To open this panel click Show Hide in the Command Script Editor panel If a command is not logged open the relevant folder and select the button corre sponding to the command click Rebuild Command History and then click Hide The command of interest should now appear in the list 12 5 2 Building a Command Script To build a command script from commands logged in the Command History list you will need to select and copy the commands of interest In
248. t D 1 3 Conversions to and From PDB Format pdbconvert This section describes the command line utility version of the program that converts files between PDB MacroModel and Maestro formats For information on PDB conversion within the Maestro GUI see Section 3 1 3 on page 21 Syntax pdbconvert options ipdb imm imae inputfile opdb omm omae outputfile ipdb inputfile Input file in PDB format imm inputfile Input file in MacroModel format 200 Maestro 6 5 User Manual imae inputfile opdb outputfile omm outputfile omae outputfile Options data datafile model number no color Appendix D Utilities Input file in Maestro format Output file in PDB format Output file in MacroModel format Output file in Maestro format Read datafile for more default data Specify an input structure other than the first Color atoms by type not error code no dup conect Don t take duplicate CONECT records to mean multiple bonds no renum warn h Retain atom indices from the MacroModel file Include hydrogens in missing atom and unrecognized atom name warnings Resolution of Multiple Coordinate Sets Where multiple atomic coordinates exist for a single PDB entry Maestro chooses the atoms with the highest occupancy ratio Conversion Error Codes for pdbconvert When running pdbconvert from UNIX you will receive numerical messages 2 1 0 indicating the status of an attempted PDB conversion These m
249. t and displayed See the Jaguar User Manual for details Maestro 6 5 User Manual 131 Chapter 11 Surfaces 11 4 The Surface Table Panel The Surface Table panel is used to create import modify and view surfaces and to view and modify surface properties To open the Surface Table panel choose Show Surfaces Table from the Surfaces submenu of the Display menu Data and settings displayed in the Surface Table panel are associated with the entry whose name appears in the Entry text field The scratch entry is not part of a project and thus cannot be used The entry must be included in the Workspace for the surfaces to be visible To show volume and surface data for a different entry either type the entry s name directly into the Entry text box or click Choose and select the desired entry in the Choose Entry dialog box The Volumes Surfaces For The Chosen Entry list displays volumes and surfaces for the named entry Volume names are left justified Surface names are indented When Sort By is set to Volume each surface appears after its volume but before the next volume in the list When Sort By is set to Name all surfaces appear first sorted alphabetically followed by all volumes sorted alphabetically Below the Sort By section is a Name text field in which you can change the name of the selected surface or volume The information and controls in the lower portion of the panel depend on whether a surface or a volume is selected When
250. t box navigate to it in the Directories list or click Launch Directory or Current Directory to select the directory from which you launched Maestro or the current working directory The path and the directory and file lists are updated for the chosen directory 24 Maestro 6 5 User Manual Chapter 3 Importing and Exporting Structures and Data Selecting a file If the file exists you can select it in the Files list or enter its name in the File text box If you want to export to a new file enter the name in the File text box You can specify an absolute or relative path in the File text box in addition to the file name Appending or overwriting files To append a structure to an existing file select Append Tf the file exists and you do not select Append it is overwritten Saving graphical information If you are writing a Maestro file you can select Save Graphical Information to store the molecular representation information for the structure you are saving This option is ignored for other file types Specifying the source of the structures The Export panel can be used to save structures directly from the Workspace or to write out files containing structures associated with one or more project entries To write out the Workspace to a file select Workspace in the Structure Source To Be Exported section This is equivalent to writing the included entries To use the entries that are selected in the Project Table as the content for the exp
251. t button You can also pick residues to display using the Display only this residue button in the toolbar ED In the lower section you can apply the operation to the following structural units using the buttons under the operation heading Protein Backbone Protein Sidechains Water Molecules Non polar H Atoms Polar H Atoms The tools in the lower section are also available from the toolbar as the Display Only Also Display and Undisplay button menus From these menus you can choose any of the structural units listed above and you can choose All All Hydrogens or Select to open the Atom Selection dialog box and select the atoms to display or undisplay 70 Maestro 6 5 User Manual Chapter 7 Manipulating Structures Maestro provides a range of tools for manipulating structures in the Workspace In addi tion to coordinate transformations such as rotation and translation there are tools for centering a structure on a particular atom zooming in on a structure and arranging struc tures in a rectangular grid which is called tiling Transformations can be carried out globally or locally Global transformations move all of the atoms in the Workspace together as a unit They do not change atom coordinates only the orientation and location relative to the viewer Local transformations move a user defined subset of atoms relative to the rest of the atoms in the Workspace and therefore must change the atom coordinates Tili
252. t is selected the cursor in the Workspace appears as a box and the object is indicated by a letter appearing under the cursor box The letters A B R C M and E represent in order Atoms Bonds Residues Chains Molecules and Entries You do not need to select the Pick button before choosing an item from the Pick menu Choosing an item automatically selects the Pick button 5 2 The Atom Selection Dialog Box If you want to make atom selections based on more complex criteria such as selecting all the carbon atoms in a protein backbone you can use the Atom Selection dialog box The Atom Selection dialog box allows you to select atoms by defining complicated ASL expressions without the need to understand the ASL syntax To open the Atom Selection dialog box click Select in the relevant section of any panel The Atom Selection dialog box is modal you must dismiss it before you can perform any other operations with the exception of rotation and translation of structures in the Work space and picking The features of the dialog box are described below 54 Maestro 6 5 User Manual Chapter 5 Selecting Atoms Atom Selection Select To Delete Notation sequence Residue Type Residue Number atom reside Motecue Qn entry sena A Classification Backbone Side Chain secondary Structure Subtract Intersect Atoms Matching 96 E Show markers res num gt 200 Proximity lg Set Undo Sec Clear Invert
253. t job status StatusTime The time at which Status was last updated StopTime The time at which the calculation stopped StructureMonitorFile The name of the monitoring file holding the molecular structure StructureOutputFile The name of the file holding the final molecular structure User The user name under which job was launched To list the complete database record for a job enter the command SCHRODINGER jobcontrol dump jobid 14 4 2 Purging the Job Database Normally when running jobs from Maestro s project facility the database record for a job is cleared once the job is incorporated into a Maestro project Not all jobs can be incorpo rated however for this and other reasons job records might not get deleted automatically and the jobdb directory can become quite large over time The job control utility can be used to purge the job database of records for completed jobs For example the following command purges the entire database SSCHRODINGER jobcontrol delete all This command only affects completed jobs running jobs cannot be deleted However you should be careful not to delete completed jobs whose output you still intend to incorporate into a Maestro project The job database is automatically checked for jobs that have finished whenever you start a new job If the job is older than a threshold time it is deleted from the database You can set this threshold time in the environment variable SCHRODINGER_JOBDB_CLEANUP
254. th a typical grid spacing of 1 A within the box Next van der Waals energies and x y and z electrostatic field components are computed at each of the grid points Receptor atom partial charges and van der Waals parameters are taken from the OPLS AA force field A probe is represented by a van der Waals sphere of radius 1 5 A well depth 0 2 kcal mol and point dipole moment 2 3 Debye The probe s point dipole is oriented along the electric field to give a minimum negative electrostatic energy and is offset from the vdW body which is located at the grid point and represents the oxygen atom of a water molecule toward the center of an optimally oriented O H bond A smoothing procedure is applied during the calculation of the receptor s electric 128 Maestro 6 5 User Manual Chapter 11 Surfaces field to avoid artificial singularities The hydrophilic and hydrophobic grid values are then determined from Eqs 1 and 2 Finally the hydrophilic and hydrophobic grids are read by Maestro which contours the grids at the empirically selected default isovalues cited above 6 and 0 5 kcal mol and displays the corresponding hydrophilic and hydrophobic volumes as surfaces 11 2 3 Specifying a Structure to Be Mapped To create a sitemap of a structure you must first include the structure in the Workspace The structure must belong to an entry in the current project you cannot map structures from more than one entry or from a scratch entry
255. the Entry menu To redisplay all entries choose Show All from the Entry menu The display of entries does not affect either the subsequent selection or inclusion of entries though of course you can only use the mouse to select or include the entries that are displayed in the Project Table 8 5 3 Renaming Entries When importing entries from files incorporating entries from jobs merging entries with identical names duplicating entries or disassociating entries Maestro automatically assigns new entry names You do not have to accept the automatically assigned names you may rename the entries using one of the methods described below Maestro 6 5 User Manual 89 Chapter 8 Projects To change the name of a single entry 1 Double click the entry name if the entry is not selected or single click the name if the entry is selected 2 Type in the new name 3 Press ENTER To rename multiple entries with the same base name 1 Select the entries to be renamed 2 Click the entry name for one of the entries 3 Type in the new name 4 Press CTRL ENTER Maestro automatically adds incremental numbers to the name you assign to make the entry names unique 8 5 4 Duplicating Entries To duplicate entries select the entries and choose Duplicate from the Entry menu Maestro copies the entries to the end of the Project Table The new entries retain the same base name as the originals but have dupn appended The number n indexes the
256. the Molecular Surface panel and the Extended Radius Surface panel Since the van der Waals surface is by definition built directly on the van der Waals spheres a probe radius setting is not needed for this panel The value in the Probe Radius text box controls the radius of the probe sphere that is rolled over the van der Waals surface of the molecule The default probe radius of 1 4 corresponds to water Create Surface To start the molecular surface generation click Create Surface During this time Maestro is inoperative and no user interaction is possible For large surfaces and high quality surface generation can be time consuming 124 Maestro 6 5 User Manual Chapter 11 Surfaces Molecular Surface surfacemolecular IE Name Molecular Surface Atoms for surface display ASL Sige All Select W Pick Entries WE Show markers Surface context 4 Entry Molecule Q Selected atoms Image quality Low lt Medium lt High Probe radius 1 40 Create Surface Hide Help Figure 11 1 The Molecular Surface panel 11 1 2 Molecular Structure Surfaces In the Molecular Surface panel you can generate a surface that follows the molecular surface but is smoother than the CPK surface The best known type of molecular surface is the Connolly surface Imagine rolling a ball representing a solvent molecule over the assembly of spheres constituting the van der Waals surface Where the out
257. the Project Table Each row contains the row number the title the entry s Workspace inclusion state the In column a button to open the Surfaces panel if there are surfaces associated with the entry the entry name and any properties associated with the entry If there are no surfaces associated with any entry the Surf column of the Project Table is empty You control which entries are displayed in the Workspace from the Project Table You can use entries as input for most of the computational programs Glide Jaguar LigPrep MacroModel Prime QikProp and QSite You can select entries as input for the ePlayer which displays the selected structures in sequence You can duplicate combine rename split and sort entries create properties for entries import structures as entries and export entries in various formats Although the Project Table does not have spreadsheet capabili ties you can export properties to and import properties from a spreadsheet Maestro 6 5 User Manual 11 Chapter 2 Maestro Overview Project Table table test JEJE Table Select Entry Property ePlayer 2 selected i5 mol 0008 mol_0008 imp1 o lt Slmol 0008 mol 0008 impi inci O 0 I NNNM Figure 2 2 The Project Table panel When you build molecules in the Workspace they constitute the scratch entry until you choose to save the structures as project entries The scratch entry is not saved with the project unless you explicit
258. the atoms to label When you modify the label contents or appearance you can update all labels with the new definitions by clicking Update Existing Labels If you want to remove some or all labels select Remove in the Mode section The Label atoms section is relabeled Clear Labels Use the tools in this section to remove labels When you select Remove the label composition is no longer relevant You can also label atoms from the toolbar To apply a single property from a subset of the full range of properties to all atoms use the Label Atoms button menu P al To apply the current labeling scheme by picking use the Label Picked Atoms button menu 4 Double click this button to apply the current labeling scheme to all atoms From the button menu you can choose Composition to open the Atom Labels panel with the Composition folder displayed you can choose Select to open the Atom Selection dialog box to select the atoms to label and you can choose Delete Labels to delete all labels If you want to customize the appearance and position of the label you can do so in the Label folder of the Preferences panel See Section 12 2 5 on page 141 for information 6 4 Displaying and Undisplaying Atoms The Display Undisplay Atoms panel allows you to select the atoms that are displayed or are not displayed in the Workspace For example you can hide from view all atoms user defined atom subsets or predefined subsets such as protein backbones
259. the lower portion of the panel The legend at the top of the panel describes the colors that will be applied and the criteria used to apply them Once you have selected a scheme use the picking tools to select the atoms you wish to color or click the All button to apply the selected color scheme to all atoms in the Workspace You can also apply a color scheme to all atoms in the Workspace from the Color all atoms by scheme button menu in the toolbar amp When you click and hold on this icon a menu is displayed from which you can choose the scheme The color scheme is applied when you make your menu choice The schemes are described in the Color Scheme folder 6 2 Changing Molecular Representations The Molecular Representation panel contains four folders Settings Atoms Bonds and Ribbons The Ribbons folder contains controls for representing the structure of proteins The first three folders contain controls for setting molecular representation for the atoms and bonds in the Workspace and for setting the molecular representation in which subsequently drawn atoms and bonds are displayed Using the controls in these folders you can choose to change the molecular representation for all atoms and bonds in the Workspace for only the atoms currently in the Workspace or for only the bonds currently in the Workspace You can also use the shortcuts available in the toolbar to change the molecular representation To open the Molecular Represent
260. the mouse or the tools in the Entry menu Selected entries can be renamed duplicated combined split deleted exported and included in the Workspace or a movie of the structures associated with entries can be made with the ePlayer Some operations on selected entries are mapped to shortcut keys which are described in Table 8 2 on page 84 Selection states are persistent across Maestro sessions entries that are selected when a project is closed will still be selected the next time that project is opened When new entries are imported or incorporated into the Project Table they are automatically selected Maestro 6 5 User Manual 85 Chapter 8 Projects 8 4 1 The Select Menu The Select menu provides tools for selecting entries The first three items All None and Invert select all entries no entries deselect all entries and invert the selection select the unselected entries and deselect the selected entries Only Add and Deselect open the Entry Selection dialog box so that you can select entries by a combination of properties The Filter submenu allows you to choose a named filter that is used to select entries and to edit named filters Filters are defined in terms of Entry Selection Language ESL expres sions and do not constitute a fixed set of entries Whenever the filter is used the ESL expression is applied to the current contents of the Project Table For more information on ESL see the Maestro Command Reference Manua
261. the selection To select all plots press ALT A to deselect all plots press ALT U You can also select plots from the Plot menu or from the list of plots in the Plot Settings panel To open this panel choose Plot Settings from the Settings menu or press ALT P As with entries in the Project Table you can select plots and display plots independently When you have selected a group of plots you can display only those plots add them to the display or remove them from the display by using the commands on the Plot menu Maestro 6 5 User Manual 115 Chapter 10 Plotting 10 2 2 Panning and Zooming The zoom bar controls operate on one or more selected plots If you do not have any plots selected then none of the zoom bar controls are active If you have one plot selected then the zoom controls display the plot s current zoom If you have more than one plot selected and all of the plots have the same zoom that zoom is displayed Otherwise the zoom controls are blank When you have multiple plots selected the panning and zoom controls operate within each plot to pan the plotted data with respect to the axes or zoom in on the plotted data The first items in the zoom bar are edit controls for directly setting the zoom for both hori zontal and vertical directions Below the edit controls are a series of arrow buttons for panning the displayed region of the selected plots Following the arrow buttons is a Reset button This button restores th
262. thin a specified distance from a selection of atoms Click Limit to open the Limit Surface panel Select the Limit Surface viewasl EEIE Limit to ASL ASL atom entrynum 1 Clear All Select W Pick Entries WE Show markers Distance 2 000000 A Set Delete Hide Help Figure 11 8 The Limit Surface panel Maestro 6 5 User Manual 135 Chapter 11 Surfaces atoms using the tools in the Limit To ASL section enter a value in the Distance text box and click Add The limit is applied to the surface and the Add button changes to Set You can change the atom selection and click Set to apply a new limit To remove the limit click Delete Deleting surfaces To delete the surface or volume that is currently selected in the Volumes Surfaces For the Chosen Entry list click Delete 11 4 4 Importing Surfaces To import a vis or plt file from the Surface Table panel you must specify the entry with which the imported data should be associated Click Choose to open the Choose Entry dialog box and select an entry Then click the Import button The Import Surface Volume File dialog box is displayed Choose from the list of available plt and vis files or navigate to another directory and then choose a file You can also open this dialog box by choosing Import Surface Volume from the Surfaces menu of the main menu bar When you import a surface or volume file the surfaces and volumes are already named To ch
263. ting file formats MacroModel 199 Molina ala 200 PDBi 200 SD iia da 202 using Babel iaia 19 coordinates updating in FI Copy Property panel 98 copy and paste iii 97 CPK representation applymg io sila laicale 61 as van der Waals surface 126 Mod Bruni nit 64 customization PEISPECUVE raid 147 stereo viewing ii 146 with command scripts 153 Workspace appearance 145 See also preferences 212 D Delete Property dialog box 99 dihedrals measuring sss 103 directories changing in Maestro 4 creating with Make Dir 78 default installation setting 137 Display Options panel Background folder 145 Fog folder eene iter 149 Perspective folder 148 Stereo folder costes 147 Display Undisplay Atoms panel 70 distances measuring ii 103 Draw mode iii 36 dummy AtomS iii 50 defining for measurements 107 E electrostatic potential displaying on a SUT ACE cantan ill 134 element Changing eee 38 ua D M 11 adding properties t0 95 COMDE sssi isis 90 copying properties eee 98 creating
264. toms for Transformation a 43 12 2 Selecting a Rotation Center ciem sa 74 7 3 Tine Multiple Entries sini n D e e eros 74 iv Maestro 6 5 User Manual Contents Chapter 8 o1 Me 75 8 1 Project Operations o eese been e eire rte d ge Dar ee Due RE pau Benue 75 8 1 1 Creating and Opening Projects onere idiotas 75 8 1 2 Saving and Closing Projects iu rette rte 76 8 1 3 Deleting Projects idee lai 76 8 1 4 The Project Selector Panel Sissi ai 77 8 1 5 Amnotating a Project nvidia adas 78 8 2 Adding Entries to 8 Projeet cile 78 8 2 1 Importing Structures From a File cociendo it 78 8 2 2 Creating Entries From Workspace Structures eese 79 8 2 3 Incorporating Entries From Job Output eere 79 8 2 4 Merging Entries From Another Project i 79 8 3 The Project Table Panel 5 2 reete eere t ee Redes 80 83 1 The Project Table Toolbar siii teret tete 81 8 32 The Project Table Menus i iuter dani rotor eerie esee eerie ints 82 8 3 3 Mouse Functions in the Project Table eene 83 8 3 4 Project Table Shortcut Keys erre 84 8 3 5 Configuring the Projeet Table oi ce Rte erret 84 8 3 6 Finding Text in the Project Table eterne tend 85 8 4 Selecting Project EDUIGS cere ro cre eter beni Eee lena 85 8 4 T The Select Ment eie erede ele dc edere peter 86 8 4 2 The Entry Selection Dialog BOX iii ies 86 8 4 3 Selecting
265. tro allows 36 Maestro 6 5 User Manual Chapter 4 Building Structures you to violate the valency of an atom in Draw mode so that you can change it to an atom of some other element The basic operations of Draw mode are described below To begin drawing with the currently selected element click the Draw button f The Draw button appears indented indicating that you are in Draw mode The default element is carbon To place an atom click in the Workspace The atom appears as an asterisk enclosed in a purple cube The cube indicates that the atom is active which means that it will be automatically connected to the atom that is placed next Each subsequent click in the Workspace places another atom and bonds it to the previous atom with a single bond To finish drawing click the active atom The cube vanishes To start drawing from another location in the structure deactivate the active atom by clicking on it then click on the atom that you want to start drawing from This atom becomes the active atom To connect the active atom to an existing atom click the existing atom e To create a multiple bond between the active atom and an adjacent atom click the adjacent atom Another bond is added between the two atoms To change the element that you are drawing with select the element from the Draw button menu The next new atom you place will be an atom of the new element If you connect existing atoms of a different
266. try markers or Display included entry markers Plot Settings plotxysettings EEE Piot Series x Axis Y Axis Plot name SASA W Plot displayed Caption text SASA vs Title Caption position lt Top 4 Bottom W Display caption W Display plot name in caption _ Display selected entry markers J Display included entry markers W Display point labels J Display legend Figure 10 4 The Plot folder of the Plot Settings panel 118 Maestro 6 5 User Manual Chapter 10 Plotting Displaying Data Point Labels If Display point labels is selected labels are displayed for data points that have labels For frequency plots currently only the exact position of the point on the x axis is available Displaying a Plot Legend To display a plot legend that shows which lines and points correspond to each data series select Display legend 10 3 2 Operating on Plot Series The tools in the Series folder allow you to manipulate attributes of the actual plot line and to modify the Workspace selection based on the entries included in a particular plot series Selecting a Series The series available for the selected plot are listed at the top of the folder To perform operations on a series select the series in the list Information for the selected series is displayed in the lower portion of the Series folder i mix Prot Series X Axis Y Axis Series New Edit Delete
267. ube and Ball amp Stick representations It also provides a quick means of applying a representation to all atoms to view the changes made To change the default representation so that any subsequently placed atoms use the new representation select a representation from the Default Representation to menu at the top of the folder Changing the default representation does not affect the representation of any atoms or bonds currently in the Workspace You can adjust the parameters of the representations using the sliders in the Rendering section and apply the representation using the buttons If the representation is already selected changes made using the sliders take effect immediately The seven slider controls have the following functions e Wire Width pixels adjust the width of the lines used to represent bonds in the Wire representation e CPK Percentage change the volume of the spheres in CPK mode as a percentage of the van der Waals radius Tube Radius A change the radius of the tubes in Tube mode Ball Percentage change the volume of the spheres in Ball amp Stick mode as a per centage of the van der Waals radius Stick Radius A change the radius of the sticks in Ball amp Stick mode e Moving Resolution change the resolution of the ball rendering during translation and rotation A low resolution can speed up translations and rotations Resting Resolution change the resolution of the ball rende
268. uct releases and software updates Consult the web site for the most recent information on a product 15 5 Technical Support If you have questions that have not been answered from any of the above sources contact Schr dinger using the information below Generally e mail correspondence is best because you can send relevant machine output Schr dinger E mail help schrodinger com USPS 1500 SW First Ave Suite 1180 Portland OR 97201 Phone 503 299 1150 Fax 503 299 4532 WWW http www schrodinger com FTP ftp ftp schrodinger com 182 Maestro 6 5 User Manual Chapter 15 Help When sending e mail messages please include the following All relevant user input and machine output Software purchaser company research institution or individual Primary software user Computer platform type Operating system with version number Software version number Maestro version number mmshare version number Much of the machine and system information listed above can be produced by entering the following command at a shell prompt SSCHRODINGER machid Maestro 6 5 User Manual 183 Chapter 15 Help 184 Maestro 6 5 User Manual Appendix A The Maestro File Format All Schr dinger products use the Maestro file format as their primary method of storing molecular structure information The Maestro file format is extensible That is users and third party programs can add additional fields that will be accept
269. ue for the function and displaying the surface that corresponds to that value The value is called an isovalue and the surface is called an isos urface Generated surfaces are incorporated into the Project Table and are displayed in the Work space by default when the associated entry is included Surface data for any entry can be viewed using the Surface Table panel From this panel you can change surface display properties such as transparency display style and color 11 1 Generating Surfaces From the Surfaces submenu of the Display menu in the main menu bar you can generate three kinds of surfaces that have similar characteristics molecular surfaces Connolly surfaces van der Waals surfaces and extended radius surfaces Surfaces can only be generated for project entries If you try to generate a surface for the scratch entry you will be prompted to create a project entry from the scratch entry Each surface is associated with only one entry but an entry may have zero or more surfaces 11 1 1 Surface Generation Controls Most of the surface generation settings are common to the Molecular Surface panel the Extended Radius Surface panel and the VDW Surface panel All the settings are discussed below Name You can name the surface by entering the name in the Name text box If an entry has more than one surface each surface name for that entry must be unique Maestro 6 5 User Manual 123 Chapter 11 Surfaces Atoms For S
270. ultiple lines or Thickness to display multiple bonds as thicker lines as in earlier versions of Maestro Show Bond Orders You can choose when to display multiple bonds Automatically means that bond orders are displayed at high zoom but are not displayed at low zoom The threshold for the display of bond orders can be changed with the Maestro command repall borderscale value The default for value is 30 and repre sents the width of the portion of the structure visible in the Workspace e Smoothing You can smooth the lines that represent bonds Smoothing Wire bonds especially enhances the viewing of larger structures However smoothing can pre vent multiple bonds from being displayed correctly in the Thickness representation If you do not see thick bonds deselect this option Maestro 6 5 User Manual 63 Chapter 6 Displaying Structures To apply the new representation use the picking tools or the Select button to select bonds or click All to select all bonds You can also apply a molecular representation using the Draw bonds in wire and Draw bonds in tube buttons in the toolbar O Q Click either of these buttons to pick the object to apply the representation to Double click either button to apply the representation to all atoms You can choose the object to pick from the button menus 6 2 3 Changing Representation Attributes The controls in the Settings folder allow you to customize the appearance of the Wire CPK T
271. urface Display The surface is displayed only for the atoms specified in the Atoms For Surface Display section of the panel You can select atoms by picking in the Workspace by entering an ASL expression in the ASL text box by clicking All or by clicking Select and using the Atom Selection dialog box If you want to reset the atom selection click Clear If you have Show Markers selected the atoms you select are marked in the Workspace Surface Context The surface is actually generated for the atoms specified in the Surface context section but only the portion of the surface defined by the Atoms for surface display is displayed If you choose Entry or Molecule the surface is generated for the entries or molecules of which the atoms selected for surface display are a part If you choose Selected Atoms the surface is generated only for the atoms selected for surface display and appears as a complete surface You can also limit the surface dynamically once it is created using the Limit Surface dialog box See Section 11 4 3 on page 135 for details Image Quality In the Molecular Surface panel you can set the quality of the image to Low Medium or High These controls set the grid spacing for surface generation The high quality surface is smoother but takes longer to generate The van der Waals and extended radius surfaces do not use grids so there is no corresponding image quality section Probe Radius This setting appears only on
272. urface Table panel 133 Color Scheme folder 134 Drawing folder 134 surfaces appearance Of 132 atoms for display of 124 changing isovalue 135 color schemes sese 134 COnnOll ys uen niece tics 125 COMO 124 creating from existing volume 155 deleting iii 136 displaying and undisplaying 132 extended radius ss 125 generating ie 123 124 hydrophilic hydrophobic 127 image Quality sess 124 importing 131 136 lima ting aie 135 217 Index T lecul r autori risi 125 irr 123 DIODE TARIUS RR PRE saves 124 Sitemap cerrar ans 127 131 tranSparency sses centem 133 van der Waals sess 126 Sybyl Mol2 file format converting TO DEOTI iioc terit triti rtt rs 200 T templates for pdbconvert 202 temporary files POMOVAl iii 162 writing to output directory 174 terminal atoms deleting 51 text finding in the Project Table 85 TIEF files ttt 122 139 tiling structures esee 74 toolbar Build panel in 31 32 All arnie 7 10 main hiding and redisplaying 154 ln siok
273. ut file is specified structures are written to the file propfilter mae v Show the version number of this utility Filter conditions must be specified in the form name op value or just name Here name is the name of a property or descriptor name For QikProp properties the standard CSV file header name may be used e g MW or nstars or dip 2 V The internal Maestro property names may also be used e g r qp mol wt or i qpn starsorr rp d2ov op The conditional operator op must be one of the following V gt lt lt l I and it must be surrounded by white space The and operators perform pattern matching using regular expressions If a condition is simply name then the named property is required to exist but it may have any value Tf filter conditions are supplied in an input filter file there must be one condition per line Lines that start with are treated as comments Blank lines are ignored D 3 Display of Properties proplister List properties in Maestro formatted files Syntax proplister options input files Options a Report all the properties found in the input files Write properties to a CSV file Maestro 6 5 User Manual 205 Appendix D Utilities h Show usage summary 1 List the names of all the properties found in the input files n List the property names for which user friendly names are known Input files are ignored p property names Name
274. w All from the Property menu As well as reducing the amount of data displayed in the Project Table limiting the displayed properties can be used to limit the properties that are exported to a spreadsheet file 8 7 5 Moving and Resizing Property Columns You can move and resize individual columns in the project table with the mouse Dragging a column border with the middle mouse button resizes the column Dragging the column heading moves the column You can only move columns that are in the scrollable area By default the Title property is in the fixed area and the Entry Name property is in the scrol Show Property A Show All Hide All Property Family QikProp Show Hide Show Cancel Figure 8 12 The Show Property dialog box 100 Maestro 6 5 User Manual Chapter 8 Projects lable area You can swap these two columns by choosing Swap Title Entry from the Columns submenu of the Table menu You can also resize all columns to fit the width of the data to fit the width of the data and the heading or to a fixed width by choosing the appropriate item from the Columns button menu or the Columns submenu of the Table menu 8 7 6 Exporting and Importing Data Maestro does not provide spreadsheet capabilities However you can export data to a spreadsheet file operate on the properties and re import the modified data These capabil ities are available from the Import and Export submenus of the Tab
275. wers first in the online help which is presented in the Help panel The Help panel contains two folders for locating help topics the Search folder and the Categories folder Below these folders the topic name appears in the Topic text box and the help topic is displayed in the text area below the topic title Most topics contains a list of contents at the top that you can click to go to the relevant section and a list of related topics at the end that you can click to select a new topic For general information open the Help panel and start a search To open the Help panel choose Help from the Help menu or press ALT H in the Workspace For help on a particular panel s features click the Help button in the lower right corner of the panel The Help panel opens with the relevant topic displayed 15 1 1 Locating a Topic by Searching The Search folder allows you to search for a topic using a search string Type the string in the Search For text box and press the RETURN key or click the Search button If there are any topics in the help file that contain the search string you entered they are listed in the Topics which match search list The search results are sorted in alphabetical order By default the last entry in the list is highlighted This does not mean that the highlighted topic most closely matches the query word To view a topic double click on its name in the list or click on the name once and then press the RETURN key You
276. xample Maestro File Below is extract from a Maestro format file The complete file is not shown Where data has been exempted it has been noted with an ellipse The text in italic type is provided as annotation and is not a part of the file Maestro 6 5 User Manual 187 Appendix A The Maestro File Format The first block in the file is unnamed This contains required information that is relevant to the whole file s m m2io version 1 0 0 f m ct The CT block Each structure in the file is contained in such a block This is a full block s_m title The only CT level data name A string value representing the title of this structure The separator between the data names and data values Cyclohexane The value of the title data item m atom 18 The start of the atom block for this CT block There are 18 atoms in this block i m mmod type The MacroModel atom type r m x coord The X coordinate r m y coord The Y coordinate r m z coord The Z coordinate i m residue number The residue number s m insertion code The PDB insertion code s m mmod res The one letter MacroModel residue code s m chain name The PDB chain name i m color The color for this atom r m chargel The partial atomic charge r m charge2 The partial atomic charge s m pdb residue name The PDB residue name s m pdb atom name The PDB atom name Ss m grow name The name used by the Maestro structure builder 188 Maestro 6 5 User Manual i m atomic nu
277. y cannot be part of the scratch entry If Show Markers is selected an orange box is displayed in the Workspace to mark the mapping box region The box margin provides a buffer around the minimal defined mapping box enclosure Adding a buffer region may be useful if you are investigating modification of the ligand to obtain a better fit in the active site and would like to generate a surface large enough to show how modified or added atoms would interact To alter the box margin enter a value into the Box Margin text box If you have defined the mapping box region using fillres in an ASL expression you may want to set the box margin value to zero 11 2 5 Running the Sitemap Job In contrast to the generation of other types of surfaces site mapping is run as a job You must supply a unique name for the job in the Job text box After you have configured the Sitemap panel settings you can chose to either run the job or to simply write out the job files so that you can run the calculation later To start the calculation click the Start button The Monitor panel is displayed and the job s progress is printed to the window in the upper portion of the panel To write the job files without running the job click the Write Job Files button You can use these files to subsequently launch the calculation from the command line If the job finishes while it is being monitored the results are automatically incorporated and the sitemap is displayed I
278. yed in the Workspace By default any changes in the structure are also temporary However you can save changes during play by selecting Save workspace at each step Superimpose Entry One instance in which you may find the ePlayer very helpful is in superimposing entries onto each other or onto a reference structure For instance when viewing ligands you might want to view them superimposed on a receptor You can do this by fixing the receptor in the Workspace but selecting only the ligands If you choose On Previous Entry each entry is superimposed on the previous entry in the series If you choose On Reference Entry you must specify a reference entry either by typing its name in the Reference text box or clicking the Choose button and choosing an entry from the list The reference entry can be any entry but to view it during play you must fix it in the Workspace ePlayer Options eplayer General Speed 0 00 Jseconas per entry J Save Workspace changes during continuous play Superimpose entry 4 None lt On previous entry ww On reference entry r Run script at each step None Q Current script From file ud Hide Help Figure 8 6 The ePlayer Options panel 94 Maestro 6 5 User Manual Chapter 8 Projects If you choose to superimpose structures in Step mode the project synchronization mode that you have selected in the Preferences panel is applied If you have chosen Aut

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