Maestro Overview
Contents
1. tereads a Python file so that the next time you use the pythonrun com mand it uses the updated version of the module You can also use the alias pyimp From the Maestro Scripts menu you can install manage and run Python scripts For more information on the Scripts menu see Section 13 1 of the Maestro User Manual A variety of Python scripts is available from the Script Center on the Schr dinger web site For more information on using Python with Maestro see Scripting with Python Command Scripts All Maestro commands are logged and displayed in the Command Script Editor panel This means you can create a command script by performing the operations with the GUI controls copying the logged commands from the Command History list into the Script text area of the panel then saving the list of copied commands as a script To run an existing command script 1 Open the Command Script Editor panel from the Edit menu in the main window 2 Click Open Local and navigate to the directory containing the desired script 3 Selecta script in the Files list and click Open The script is loaded into the Script window of the Command Script Editor panel 4 Click Run Script Command scripts cannot be used for Prime operations Maestro 8 0 Overview 27 28 Command Script Editor le Command history alias pyrun pythonrun alias pyimp pythonimport thoneval Select All Deselect All Copy Selection To Script W Log commands2. The 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 the following e Pick option menu Allows you to choose Atoms Bonds Residues Chains Molecules or Entries then click on an atom in the Workspace to perform the action on all the atoms in that structural unit The Pick option menu varies from panel to panel because not all object types are appro priate for a given operation For example some panels have only Atoms and Bonds in the Pick option menu e All button Performs the action on all atoms in the Workspace e Selection button Performs the action on any atoms already selected in the Workspace Maestro 8 0 Overview 25 26 e Previous button Performs the action on the most recent atom selection defined in the Atom Selection dialog box e Select button Opens the Atom Selection dialog box e ASL text box Allows you to type in an ASL expression for selecting atoms ASL stands for Atom Specification Language and is described in detail in the Maestro Command Reference Manual e Clear button Clears the current selection x e Show markers option Marks the selected atoms in the Workspace For example to label atoms with the Label Atoms panel 1 Choose Atom Labels from the Display menu 2 In the Composition tab select Element and Atom Number 3 In the picking tools section at the top of the panel y
3. Choose Show Table from the Project menu Press CTRL T The Project Table panel contains a menu bar a toolbar and the table itself Maestro 8 0 Overview 16 The Project Table Toolbar The Project Table 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 See page 9 for a description of the types of toolbar buttons The buttons are described below a Sl BR i F E Jel 144 I4 Find Open the Find panel for locating alphanumeric text in any column of the Project Table except for the row number Sort Open the Sort panel for sorting entries by up to three properties Plot Open the Plot panel for plotting entry properties Import Structure Open the Import panel for importing structures into the project Export Structure Open the Export panel for exporting structures to a file Columns Choose an option for adjusting the column widths Select only Open the Entry Selection dialog box for selecting 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 th
4. M Hide transformation commands m Script hydrogentreat All atom with No Lp AY showpanel script ad a Run Script i Expand Command Aliases Open Local Open Global Save As Close Help Figure 5 The Command Script Editor panel Macros There are two kinds of macros you can create named macros and macros assigned to function keys F1 through F12 To create and run a named macro 1 2 3 4 5 Open the Macros panel from the Edit menu in the main window Click New enter a name for the macro and click OK In the Definition text box type the commands for the macro Click Update to update the macro definition Torun the macro enter the following in the command input area in the main window macrorun Macro name If the command input area is not visible choose Command Input Area from the Display menu Maestro 8 0 Overview To create and run a function key macro 1 Open the Function Key Macros panel from the Edit menu in the main window 2 From the Macro Key option select a function key F1 through F12 to which to assign the macro 3 In the text box type the commands for the macro 4 Click Run to test the macro or click Save to save it 5 To run the macro from the main window press the assigned function key For more information on macros see Section 13 5 of the Maestro User Manual Specifying a Maestro Working Directory Maestro
5. around the X axis by 90 degrees 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 selected atoms Choose an object type for displaying Double click to display all atoms Also display Choose a predefined atom category Open the Atom Selection dialog box Display residues within N angstroms of currently displayed atoms Choose a radius Open a dialog box to set a value Draw bonds in wire Choose an object type for drawing bonds in wire representation Open the Atom Selection dialog box Double click to apply to all atoms Draw atoms in Ball amp Stick Choose an object type for drawing bonds in Ball amp Stick representation Open the Atom Selection dialog box Double click to apply to all atoms Color all atoms by scheme Choose a predefined color scheme 90 4 DD xyz 4 al 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 Rotate the Workspace contents around the Y axis by 90 degrees 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 orientation location and zoom Display only Choose a predefine
6. buttons The toolbar buttons and their use are described below Maestro 8 0 Overview 23 24 i L aa Free hand drawing Choose an element for drawing structures freehand in the Workspace default C Each click in the Workspace places an atom and connects it to the previous atom Delete Choose an object for deleting Same as the Delete button on the main toolbar see page 10 Set element Choose an element for changing atoms in the Workspace default C Click an atom to change it to the selected element Increment bond order Select a bond to increase its bond order by one to a maximum of 3 Decrement bond order Select a bond to decrease its bond order by one to a minimum of 0 Increment formal charge Select an atom to increase its formal charge by one Decrement formal charge Select an atom to decrease its formal charge by one Move Choose a direction for moving atoms then click the atom to be moved Moves in the XY plane are made by clicking the new location Moves in the Z direction are made in 0 5 A 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 amp Fuse panel Open the Connect amp Fuse panel so you can connect structures create bonds between struc tures or fuse structures replace atoms of one structure with those of another Display Adjust panel O
7. can either click on a single atom or bond or you can drag to select multiple objects The right mouse button opens shortcut menus which are described in Section 2 7 of the Maestro User Manual The middle and right mouse buttons can be used on their own and in combination with the SHIFT and CTRL keys to perform common operations such as rotating translating centering adjusting and zooming Table 1 Mapping of Workspace operations to mouse actions Mouse Button Keyboard Motion Action Left click drag Select Left drag Quick Torsion adjustment and adjust ment of distance angle dihedral Left SHIFT click drag Toggle the selection Middle drag Rotate about X and Y axes Middle SHIFT drag vertically Rotate about X axis Middle SHIFT drag horizontally Rotate about Y axis Middle CTRL drag horizontally Rotate about Z axis Middle SHIFT CTRL drag horizontally Zoom Right click Spot center on selection Maestro 8 0 Overview Toggle selection Table 1 Mapping of Workspace operations to mouse actions Continued Mouse Button Keyboard Motion Action Right click and hold Display shortcut menu Right drag Translate in the X Y plane Right SHIFT drag vertically Translate along the X axis Right SHIFT drag horizontally Translate along the Y axis Right CTRL drag horizontally Translate along the Z axis Middle amp Right drag horizontally Zoom Wheel scroll Zoom In any adjust mode do adjustment Wheel CTRL scroll Adjust isovalue
8. of electron density map PrimeX In clipping planes window move clipping planes in opposite directions Wheel SHIFT scroll In clipping planes window move Shortcut Key Combinations clipping planes in the same direction Some frequently used operations have been assigned shortcut key combinations The shortcuts available in the main window are described in Table 2 Table 2 Shortcut keys in the Maestro main window Keys CTRL B CTRL C CTRL E CTRL F CTRL H CTRL I CTRL M CTRL N CTRL O Action Open Build panel Create entry Open Command Script Editor panel Open Find Atoms panel Open Help panel Open Import panel Open Measurements panel Create new project Open project Equivalent Menu Choices Edit gt Build Project gt Create Entry From Work space Edit gt Command Script Editor Edit gt Find Help gt Help Project gt Import Structures Tools gt Measurements Project gt New Project gt Open Maestro 8 0 Overview 13 14 Table 2 Shortcut keys in the Maestro main window Continued Keys Action Equivalent Menu Choices CTRL P Print Maestro gt Print CTRL Q Quit Maestro gt Quit CTRL S Open Sets panel Tools gt Sets CTRL T Open Project Table panel Project gt Show Table CTRL W Close project Project gt Close CTRL Z _ Undo Redo last command Edit gt Undo Redo CTRL Enter and exit full screen mode Workspace None occupies full screen Maestro Projects All the w
9. project Zipped projects have a prjzip extension and are read only To replace the zipped project you must first save it then zip it then copy it over the old project Zipped projects can also be linked to a web page clicking on the link to project in your browser opens the project in Maestro Starting Maestro on a UNIX Host Before starting Maestro you must first set the SCHRODINGER environment variable to point to the installation directory To set this variable enter 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 If 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 For local display you should omit display machine name After you set the SCHRODINGER and DISPLAY environment variables you can start Maestro using the command SCHRODINGER maestro options If you add the SCHRODINGER directory to your path you only need to enter the command maestro Options for this command are given in Section 2 1 of the Maestro User Manual Maestro 8 0 Overview The Maestro Main Window The Maestro ma
10. right button displays a shortcut menu Other common mouse functions are supported such as using the mouse in combination with the SHIFT or CTRL keys to select a range of items in a list and select or dese lect a single item without affecting other items The mouse wheel is supported for scrolling vertically in tables lists and text areas and can be used in combination with the SHIFT key for larger movements The wheel is also used for zooming in the Workspace and other special functions See Table 1 on page 12 and Table 3 on page 19 for summaries of mouse operations In addition the mouse buttons are used for special functions described later in this chapter These functions assume that you have a three button mouse If you have a two button mouse ensure that it is configured for three button mouse simulation the middle mouse button is simulated by pressing or holding down both buttons simultaneously Maestro 8 0 Overview 5 Starting Maestro The mechanism for starting Maestro is different for UNIX and Windows hosts This mecha nism is described for each of these host types in the following subsections Starting Maestro on a Windows Host To start Maestro double click the Maestro icon on the desktop or use the Start menu Maestro is in the Schr dinger submenu This submenu can also be used to open the release notes and the documentation index in your browser To start Maestro with a specific project double click the zipped
11. value in a table cell Include an entry in the Workspace 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 selection or inclusion state Scroll through the entries Click repeatedly in a cell to cycle through the possible val ues On Off Clear Right click anywhere in the entry If the entry is not selected it becomes the selected entry If the entry is selected the 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 Use the wheel to scroll one entry at a time hold down SHIFT and use the wheel to scroll a page at a time Maestro 8 0 Overview 19 20 Project Table Shortcut Keys Some frequently used project operations have been assigned shortcut key combinations The shortcuts their functions and their menu equivalents are listed in Table 4 Table 4 Shortcut keys in the Project Table Keys Action Equivalent Menu Choices CTRL A Select all entries Select gt All CTRL F Fix entry i
12. L X It is not affected by the inclusion or exclusion of other entries Fixing an entry affects only its inclusion you can still rotate translate or modify the structure Maestro 8 0 Overview Mouse Functions in the Project Table The Project Table supports the standard use of shift click and control click to select objects This behavior applies to the selection of entries and the inclusion of entries in the Workspace You can also drag to resize rows and columns and to move rows You can scroll vertically through the Project Table using the mouse wheel You can drag a set of non contiguous entries to reposition them in the Project Table When you release the mouse button the entries are placed after the first unselected entry that precedes the entry on which the cursor is resting 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 1 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 A summary of mouse functions in the Project Table is provided in Table 3 Table 3 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
13. Maestro 8 0 Overview O Schr dinger Press Copyright 2007 Schr dinger LLC All rights reserved CombiGlide Epik Glide Impact Jaguar Liaison LigPrep Maestro Phase Prime PrimeX QikProp QikFit QikSim QSite SiteMap and Strike are trademarks of Schr dinger LLC Schr dinger and MacroModel are registered trademarks of Schr dinger LLC MCPRO is a trademark of William L Jorgensen 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 Please note that any third party programs Third Party Programs or third party Web sites Linked Sites referred to in this document may be subject to third party license agreements and fees Schr dinger LLC and its affiliates have no responsibility or liability directly or indirectly for the Third Party Programs or for the Linked Sites or for any damage or loss alleged to be caused by or in connection with use of or reliance thereon Any warranties that we make regarding our own products and services do not apply to the Third Party Programs or Linked Sites or to the interaction between or interoperability of our products and services and the Third Party Programs Referrals and links to Third Party Programs and Linked Sites do not constitute an endorsement of such Third Party Programs or Linked Sites The Schr dinger software distribution includ
14. Table Select Entry Property ePlayer 27 106 209270 tetrahydrothiopyran 102 199450 29 110 178720 3 N O mixed heterocycles 1 2 5 oxadi azole 1 2 4 oxadiazole 70 051040 70 051040 i nf Pi Close Help Figure 3 The Project Table panel Once an entry has been incorporated into the project its structures and their data are repre sented by a row in the Project Table Each row contains the row number an icon indicating whether the entry is displayed in the Workspace the In column the entry title a button to open the Surfaces panel if the entry has surfaces the entry name and any entry properties The row number is not a property of the entry Entries can be collected into groups and the members of the group can be displayed or hidden Most additions of multiple entries to the Project Table are done as entry groups You can use entries as input for all of the computational programs Glide Impact Jaguar Liaison LigPrep MacroModel Phase Prime QikProp QSite and Strike You can select entries as input for the ePlayer which displays the selected structures in sequence You can also duplicate combine rename and sort entries create properties import structures as entries and export structures and properties from entries in various formats To open the Project Table panel do one of the following e Click the Open Close Project Table button on the toolbar ii e
15. Workspace to place an atom of that element 2 3 Click again to place another atom and connect it to the previous atom 4 Continue this process until you have drawn the structure 5 Click the active atom again to finish drawing Adjusting Properties In the Atom Properties tab you can change the properties of the atoms in the Workspace For each item on the Property option menu Element Atom Type MacroModel Partial Charge PDB Atom Name Grow Name and Atom Name there is a set of tools you can use to change the atom properties For example the Element tools consist of a periodic table from which you can choose an element and select an atom to change it to an atom of the selected element Similarly the Residue Properties tab provides tools for changing the properties of residues the Residue Number the Residue Name and the Chain Name To adjust bond lengths bond angles dihedral angles and chiralities during or after building a structure use the Adjust distances angles or dihedrals button on the main toolbar You can also open the Adjust panel from this button menu from the Display Adjust panel button on the Build panel toolbar which has the same appearance as the above button or from the Edit menu in the main window The Build Panel Toolbar The toolbar of the Build panel provides quick access to tools for drawing and modifying struc tures and labeling atoms See page 9 for a description of the types of toolbar
16. anel or close it if it is open PH Local transformation Choose an object type for transforming Open the Advanced Transformations panel Ba Maestro 8 0 Overview Undo Redo Undo or redo the last action Same as Undo on the Edit menu Changes to an arrow pointing in the opposite direction when an Undo has been performed indi cating that its next action is Redo Import structures Open the Import panel Save as Open the Save Project As dialog box to save the project with a new name Delete Choose an object type for deleting Delete hydrogens and waters Open the Atom Selection dialog box Delete other items associated with the structures in the Workspace Double click to delete all atoms Add hydrogens Choose an object type for applying a hydrogen treatment Open the Atom Selection dialog box Double click to add hydrogens to all structures in the Workspace Adjust distances angles dihedrals chiralities torsions or rotamers Choose a parameter for adjusting Display contacts Delete adjustments Open the Rotamers dialog box Fit to screen Scale the displayed structure or selected atoms to fit into the Workspace and reset the center of rotation Set fog display state Choose a fog state Automatic means fog is on when there are more than 40 atoms in the Workspace off otherwise Rotate around X axis by 90 degrees Rotate the Workspace contents
17. ction Perform an action immediately e Display Open a panel or dialog box e Object types for selection Choose Atoms Bonds Residues Chains Molecules or Entries then click on an atom in the Workspace to perform the action on all the atoms in that structural unit The object type is marked on the menu with a red diamond and the button is indented to indicate the action to be performed e Other setting Set a state choose an attribute or choose a parameter and click on atoms in the Workspace to display or change that parameter Maestro 8 0 Overview 10 Atoms p Distance Residues x 3 Angle other setting Chains object type Dihedral parameter type Molecules A 1H NMR Coupling Entries i i Delete Measurements action Select display Figure 2 Examples of button menus The toolbar buttons are described below Some descriptions refer to features not described in this document See the Maestro User Manual for a fuller description of these features Workspace selection Choose an object type for selecting Open the Atom Selection dialog box NA 4 Open a project Open the Open Project dialog box T ex Open Close Project Table Open the Project Table panel or close it if it is open Create entry from Workspace Open a dialog box in which you can create an entry in the current project using the contents of the Workspace Open Close Build panel Open the Build p
18. d atom category Open the Atom Selection dialog box Undisplay Choose a predefined atom category Open the Atom Selection dialog box Show hide or color ribbons Choose show or hide ribbons Choose a color scheme for coloring rib bons Draw atoms in CPK Choose an object type for drawing bonds in CPK representation Open the Atom Selection dialog box Double click to apply to all atoms Draw bonds in tube Choose an object type for drawing bonds in tube representation Open the Atom Selection dialog box Double click to apply to all atoms Color residue by constant color Choose a color for applying to residues Double click to color all atoms Maestro 8 0 Overview 11 12 Label atoms Choose a predefined label type Delete labels Display H bonds Choose bond type intra displays H bonds within the mole cule you select inter displays H bonds between the mol ecule you select and all other atoms in the Workspace Delete H bonds 2 RR HA Mouse Functions in the Workspace Label picked atoms Choose an object type for labeling atoms Open the Atom Selection dialog box Open the Composition tab of the Atom Labels panel Delete labels Measure distances angles dihedrals or coupling Choose a parameter for displaying mea surements Delete measurements The left mouse button is used for selecting objects You
19. e selected structures in sequence moving toward the first Stop Stop the ePlayer Play forward Display the selected structures in sequence moving toward the last Maestro 8 0 Overview Next bl Display the next structure in the list of selected structures Go to end b bl Display the last selected structure Loop ea Choose an option for repeating the display of the structures Single Direction displays struc 4 tures in a single direction then repeats Oscillate reverses direction each time the beginning or end of the list is reached The status display to the right of the toolbar buttons shows the number of selected entries When you pause the cursor over the status display the Balloon Help shows the total number of entries the number shown in the table the number selected and the number included in the Workspace The Project Table Menus e Table find text sort entries plot properties import and export structures and configure the Project Table e Select select all entries none invert your selection or select classes of entries using the Entry Selection dialog box and the Filter panel e Entry include or exclude entries from the Workspace display or hide entries in the Project Table and perform various operations on the selected entries e Property display and manipulate entry properties in the Project Table e ePlayer view entries in succession stop reverse and set the ePlayer options Sel
20. ecting Entries Many operations in Maestro are performed on the entries selected in the Project Table The Project Table functions much like any other table select rows by clicking shift clicking and control clicking However because clicking in an editable cell of a selected row enters edit mode you should click in the Row column to select entries See Section on page 19 for more information on mouse actions in the Project Table There are shortcuts for selecting classes of entries on the Select menu In addition to selecting entries manually you can select entries that meet a combination of conditions on their properties Such combinations of conditions are called filters Filters are Entry Selection Language ESL expressions and are evaluated at the time they are applied For example if you want to set up a Glide job that uses ligands with a low molecular weight say Maestro 8 0 Overview 18 less than 300 and that has certain QikProp properties you can set up a filter and use it to select entries for the job If you save the filter you can use it again on a different set of ligands that meet the same selection criteria To create a filter 1 Do one of the following e Choose Only Add or Deselect from the Select menu e Click the Entry selection button on the toolbar i 2 In the Properties tab select a property from the property list then select a condition 3 Combine this selection with the current filter b
21. es third party products For details of third party software copyrights terms and conditions see the Legal Notices for Third Party Software at SSCHRODINGER docs htmi third_party_legal htmi August 2007 Document Conventions In addition to the use of italics for names of documents the font conventions that are used in this document are summarized in the table below Font Example Use Sans serif Project Table Names of GUI features such as panels menus menu items buttons and labels Monospace SCHRODINGER maestro File names directory names commands envi ronment variables and screen output Italic filename Text that the user must replace with a value Sans serif CTRL H Keyboard keys uppercase In descriptions of command syntax the following UNIX conventions are used braces enclose a choice of required items square brackets enclose optional items and the bar symbol separates items in a list from which one item must be chosen Lines of command syntax that wrap should be interpreted as a single command File names and paths are generally represented with the UNIX conventions If you are running on Windows replace the forward slash character with the backslash character In this document to type text means to type the required text in the specified location and to enter text means to type the required text then press the ENTER key References to literature sources are given in square brackets like
22. g Help Maestro comes with automatic context sensitive help Auto Help Balloon Help tooltips an online help facility and a user manual To get help follow the steps below e Check the Auto Help text box at the bottom of the main window If help is available for the task you are performing it is automatically displayed there It describes what actions are needed to perform the task e If your question concerns a GUI element such as a button or option there may be Bal loon Help for the item Pause the cursor over the element If the Balloon Help does not appear check that Show Balloon Help is selected in the Help menu of the main window If there is Balloon Help for the element it appears within a few seconds e If you do not find the help you need using either of the steps above click the Help button in the lower right corner of the appropriate panel A browser is displayed with a relevant help topic e Use the Help menu to open the online help display manuals or visit the FAQ pages on the Schr dinger web site Maestro 8 0 Overview 31 32 If you do not find the information you need in the Maestro help system check the following sources e The Maestro User Manual e The Frequently Asked Questions page on the Schr dinger Support Center You can also contact Schr dinger by e mail or phone for help e E mail help schrodinger com e Phone 503 299 1150 Ending a Maestro Session To end a Maestro sessi
23. group and col lapse all other groups CTRL LEFT ARROW ePlayer Go to Start include first selected entry CTRL RIGHT ARROW ePlayer Go to End include last selected entry M Mark or clear mark for the current entry If the Mark property does not exist create it and set the value for the entry to true marked S Display or undisplay entry information in the Workspace This option is subject to a preference for display of single entry feedback see page 185 Building a Structure After you start Maestro the first task is usually to create or import a structure You can open existing Maestro projects or import structures from other sources to obtain a structure or you can build your own To open the Build panel do one of the following e Click the Open Close Build panel button in the toolbar Va e Choose Build from the Edit menu e Press CTRL B The Build panel allows you to create structures by drawing or placing atoms or fragments in the Workspace and connecting them into a larger structure to adjust atom positions and bond orders and to change atom properties This panel contains a toolbar and three tabs Placing and Connecting Fragments The Build panel provides several tools for creating structures in the Workspace You can place and connect fragments or you can draw a structure freehand To place a fragment in the Workspace 1 Select Place 2 Choose a fragment library from the Fragments menu 3 Click a fragmen
24. in window is shown in Figure 1 The main window components are listed below The following components are always visible e Title bar displays the Maestro version the project name if there is one and the current working directory e Auto Help automatically displays context sensitive help maestro 8 0 018 zone1 dyall phase Maestro Project Edit Display Tools Applications Workflows Scripts Help gt iR xl x lt N La jor A al gt 14 12 los Ssl FI SI EIS e Se e x Atoms 4810 4810 Entries 1 1 Res 298 Chn 3 Mol 2 Chg 1ETT impi_L_ TFGAGEADCGLRPLFEK TEKELFESYIEGR 1ETT imp1_H TVEGQDAEVGLSPWOVMLFRKSPQELLCGASLISDRWVLTAAHCLLY 1ETT impi_T X 1ETT impi_L 1ETT imp1_H PPWDKNFTVDDLLYRIGKHSRTRYERKVEKISMLDKIVIHPRYNWKE 1ETT impi_T Commands Figure 1 The Maestro main window Maestro 8 0 Overview e Menu bar provides access to panels e Workspace displays molecular structures and other 3D graphical objects The following components can be displayed or hidden by choosing the component from the Display menu Your choice of which main window components are displayed is persistent between Maestro sessions Toolbar contains buttons for many common tasks and provides tools for displaying and manipulating structures as well as organizing the Workspace e Status bar displays information about a particular ato
25. m or about structures in the Workspace depending on where the pointer pauses see Section 2 5 of the Maestro User Manual for details e Clipping planes window displays a small top view of the Workspace and shows the clipping planes and viewing volume indicators e Sequence viewer shows the sequences for proteins displayed in the Workspace See Section 2 6 of the Maestro User Manual for details e Command input area provides a place to enter Maestro commands 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 You can expand the Workspace to occupy the full screen by pressing CTRL All other components and panels are hidden To return to the previous display press CTRL again The Menu Bar The menus on the main menu bar provide access to panels allow you to execute commands and control the appearance of the Workspace The main menus are as follows e Maestro save or print Workspace images set preferences change directories enter sys tem commands save or load a panel layout set up Maestro command aliases and quit Maestro e Project open and close projects import and export structures make a snapshot and annotate a project These actions can also be performed from the Project Table panel For more information see page 14 e Edit undo actions build and modify structures define command sc
26. n Workspace Entry gt Fix CTRL I Open Import panel Table gt Import Structures CTRL N Include only selected entries Entry gt Include Only CTRL U Deselect all entries Select gt None CTRL X Exclude selected entries Entry gt Exclude CTRL Z Undo Redo last command Edit gt Undo Redo in main window In addition to these shortcut keys that can be used in the Project Table there is a range of keys that can be used both in the Project Table and the Workspace for project navigation and opera tions These keys are summarized in Table 5 Table 5 Project Table navigation and operation keys Key UP ARROW DOWN ARROW RIGHT ARROW LEFT ARROW HOME END PAGE UP PAGE DOWN SHIFT UP ARROW SHIFT DOWN ARROW CTRL UP ARROW Maestro 8 0 Overview Description Scroll the Project Table up one row Scroll the Project Table down one row ePlayer step forward include next selected entry ePlayer step backwards include previous selected entry Scroll the Project Table to the top Scroll the Project Table to the bottom Scroll the Project Table up one page Scroll the Project Table down one page Scroll the Project Table up by one group Scroll the Project Table down by one group Scroll the Project Table up by one group expand the group and collapse all other groups Table 5 Project Table navigation and operation keys Continued Key Description CTRL DOWN ARROW Scroll the Project Table down by one group expand the
27. oject directory v Project jobs directory Other specify below Directory zonel dyall glide new_tutorial glide Close Help Figure 6 The Directory tab of the Preferences panel Undoing an Operation To undo a single operation click the Undo button in the toolbar choose Undo from the Edit menu or press CTRL Z The word Undo in the menu is followed by text that describes the operation to undo Not all operations can be undone for example global rotations and transla tions are not undoable operations For such operations you can use the Save view and Restore view buttons in the toolbar which save and restore a molecular orientation Running and Monitoring Jobs Maestro has panels for each product for preparing and submitting jobs To use these panels choose the appropriate product and task from the Applications menu and its submenus Set the appropriate options in the panel then click Start to open the Start dialog box and set options for running the job For a complete description of the Start dialog box associated with your computational program see your product s User Manual When you have finished setting the options click Start to launch the job and open the Monitor panel Maestro 8 0 Overview The Monitor panel is the control panel for monitoring the progress of jobs and for pausing resuming or killing jobs All jobs that belong to you can be displayed in the Monitor panel whether or not the
28. on choose Quit from the Maestro menu To save a log file with a record of all operations performed in the current session click Quit save log file in the Quit panel This information can be useful to Schr dinger support staff when responding to any problem you report Maestro 8 0 Overview 120 West 45th Street 101 SW Main Street 3655 Nobel Drive Dynamostra e 13 QuatroHouse Frimley Road 29th Floor Suite 1300 Suite 430 68165 Mannheim Camberley GU16 7ER New York NY 10036 Portland OR 97204 San Diego CA 92122 Germany United Kingdom SCHR DINGER
29. ork you do in Maestro is done within a project A project consists of a set of entries each of which contains one or more chemical structures and their associated data In any Maestro session there can be only one Maestro project open If you do not specify a project when you start Maestro a scratch project is created You can work in a scratch project without saving it but you must save it in order to use it in future sessions When you save or close a project all the view transformations rotation translation and zoom are saved with it When you close a project a new scratch project is automatically created Likewise if there is no entry displayed in the Workspace Maestro creates a scratch entry Structures that you build in the Workspace constitute a scratch entry until you save the struc tures as project entries The scratch entry is not saved with the project unless you explicitly add it to the project However you can use a scratch entry as input for some calculations To add a scratch entry to a project do one of the following e Click the Create entry from Workspace button E e Choose Create Entry from Workspace from the Project menu e Press CTRL C In the dialog box enter a name and a title for the entry The entry name is used internally to identify the entry and can be modified by Maestro The title can be set or changed by the user but is not otherwise modified by Maestro Maestro 8 0 Overview Project Table
30. ou could do one of the following e Click Selection to apply labels to the atoms already selected in the Workspace from the previous example e Choose Residues from the Pick option menu and click on an atom in a different res idue to label all the atoms in that residue The Atom Selection Dialog Box If you wish to select atoms based on more complex criteria you can use the Atom Selection dialog box To open this dialog box choose Select from a button menu or click the Select button in a panel See Section 5 3 of the Maestro User Manual for detailed instructions on how to use the Atom Selection dialog box Scripting in Maestro Although you can perform nearly all Maestro supported operations through menus and panels you can also perform operations using Maestro commands or compilations of these commands called scripts Scripts can be used to automate lengthy procedures or repetitive tasks and can be created in several ways These are summarized below Maestro 8 0 Overview Python Scripts Python is a full featured scripting language that has been embedded in Maestro to extend its scripting facilities The Python capabilities within Maestro include access to Maestro function ality for dealing with chemical structures projects and Maestro files The two main Python commands used in Maestro are e pythonrun runs a Python module You can also use the alias pyrun The syntax is pythonrun module function e pythonimport
31. pen the Adjust panel so you can change bond lengths bond angles dihedral angles or atom chiralities Add hydrogens Choose an atom type for applying the current hydrogen treatment Same as the Add hydro gens button on the main toolbar see page 10 Geometry Symmetrizer Open the Geometry Symmetrizer panel for symmetrizing the geometry of the structure in the Workspace Geometry Cleanup Clean up the geometry of the structure in the Workspace Maestro 8 0 Overview Selecting Atoms Maestro has a powerful set of tools for selecting atoms in a structure toolbar buttons picking tools in panels and the Atom Selection dialog box These tools allow you to select atoms in two ways e Select atoms first and apply an action to them e Choose an action first and then select atoms for that action Toolbar Buttons The small triangle in the lower right corner of a toolbar button indicates that the button contains a menu Many of these buttons allow you to choose an object type for selecting choose Atoms Bonds Residues Chains Molecules or Entries then click on an atom in the Workspace to perform the action on all the atoms in that structural unit For example to select atoms with the Workspace selection toolbar button 1 Choose Residues from the Workspace selection button menu NA al The button changes to R al 2 Click on an atom in a residue in the Workspace to select all the atoms in that residue Picking Tools
32. ripts and macros and find atoms in the Workspace e Display control the display of the contents of the Workspace arrange panels and dis play or hide main window components Maestro 8 0 Overview e Tools group atoms measure align and superimpose structures assign structural fea tures and view and visualize data e Applications set up submit and monitor jobs for Schr dinger s computational pro grams Some products have a submenu from which you can choose a specific task e Workflows set up submit and monitor jobs for workflows also known as solutions These workflows generally use more than one product e Scripts manage and install Python scripts that come with the distribution and scripts that you create yourself See Chapter 13 of the Maestro User Manual for details e Help display various kinds of documentation including online help Balloon Help tooltips manuals FAQs information about Maestro and other Schr dinger products The Toolbar The main toolbar contains three kinds of buttons for performing common tasks 3 Action Perform a simple task like clearing the Workspace abs I Display Open or close a panel or open a dialog box such as the EEE Project Table panel I Menu Display a button menu These buttons have a triangle in the A lower right corner al There are four types of items on button menus and all four types can be on the same menu see Figure 2 e A
33. s current working directory is defined differently on UNIX and on Windows On UNIX it is the directory from which you started Maestro On Windows it is the user profile directory which is usually C Documents and Settings username All data files are written to and read from this directory unless otherwise specified see below You can change directories by choosing Change Directory from the Maestro menu and navigating to the desired directory or by entering the following command in the command input area see page 8 of the main window cd directory name where directory name is either a full path or a relative path When you use Maestro to launch jobs Maestro writes job output to the directory specified in the Directory tab of the Preferences panel By default this directory the file I O directory or job submission directory is Maestro s current working directory To change the Maestro working directory 1 Open the Preferences panel from the Maestro menu 2 Click the Directory tab 3 Select the directory you want to use for reading and writing files You can also set other preferences in the Preferences panel See Section 12 2 of the Maestro User Manual for details Maestro 8 0 Overview 30 _ Preferences Project Directory Label workspace File sum Builder Jobs Default directory for job startup and file i o w Maestro s current working directory wv Parent of project directory v Pr
34. t Maestro 8 0 Overview 21 22 Atom Residue Properties Frsgment Properties F Place _1 Grow Fragments Organic Fr Grow Direction forward Joining Geometry anti Close Help Figure 4 The Build panel 4 Click in the Workspace where you want the fragment to be placed To connect fragments in the Workspace do one of the following e Place another fragment and connect them using the Connect amp Fuse panel which you open from the Edit menu on the main menu bar or with the Display Connect amp Fuse panel on the Build toolbar vc e Replace one or more atoms in the existing fragment with another fragment by selecting a fragment and clicking in the Workspace on the main atom to be replaced e Grow another fragment by selecting Grow in the Build panel and clicking the fragment you want to add in the Fragments tab Grow mode uses predefined rules to connect a fragment to the grow bond The grow bond is marked by a green arrow The new fragment replaces the atom at the head of the arrow on the Maestro 8 0 Overview grow bond and all atoms attached to it To change the grow bond choose Bonds from the Pick option menu in the Build panel and click on the desired grow bond in the Workspace The arrow points to the atom nearest to where you clicked To draw a structure freehand 1 Choose an element from the Draw button menu on the Build panel toolbar f Click in the
35. this 10 Maestro 8 0 Overview 3 4 Maestro 8 0 Overview Maestro Overview Maestro is the graphical user interface for all of Schr dinger s products CombiGlide Epik Glide Impact Jaguar Liaison LigPrep MacroModel Phase Prime PrimeX QikProp QSite SiteMap and Strike It contains tools for building displaying and manipulating chemical structures for organizing loading and storing these structures and associated data and for setting up monitoring and visualizing the results of calculations on these structures This chapter provides a brief introduction to Maestro and some of its capabil ities For more information on any of the topics in this chapter see the Maestro User Manual General Interface Behavior Most Maestro panels are amodal more than one panel can be open at a time and a panel need not be closed for an action to be carried out Each Maestro panel has a Close button so you can hide the panel from view Maestro also uses dialog boxes which are modal other panels cannot be used until the dialog box is dismissed Some dialog boxes permit interaction with the Workspace so that you can select atoms and manipulate the structure Maestro supports the mouse functions common to many graphical user interfaces The left button is used for choosing menu items clicking buttons and selecting objects by clicking or dragging This button is also used for resizing and moving panels The
36. y clicking Add Subtract or Intersect These buttons perform the Boolean operations OR AND NOT and AND on the corre sponding ESL expressions 4 To save the filter for future use click Create Filter enter a name and click OK 5 Click OK to apply the filter immediately Including Entries in the Workspace In addition to selecting entries you can also use the Project Table to control which entries are displayed in the Workspace An entry that is displayed in the Workspace is included in the Workspace likewise an entry that is not displayed is excluded Included entries are marked by an X in the diamond in the In column excluded entries are marked by an empty diamond Entry inclusion is completely independent of entry selection To include or exclude entries click shift click or control click in the In column of the entries or select entries and choose Include or Exclude from the Entry menu Inclusion with the mouse works just like selection when you include an entry by clicking all other entries are excluded It is sometimes useful to keep one entry in the Workspace and include others one by one for example a receptor and a set of ligands You can fix the receptor in the Workspace by selecting it in the Project Table and choosing Fix from the Entry menu or by pressing CTRL F A padlock icon replaces the diamond in the In column to denote a fixed entry To remove a fixed entry from the Workspace you must exclude it explicitly CTR
37. y were started from Maestro Subjobs are indented under their parent in the job list The File tab shows output information from the monitored job such as the contents of the log file The Monitor panel opens automatically when you start a job If it is not open you can open it by choosing Monitor from the Applications menu in the Maestro main window While jobs are running the Detach Pause Resume Stop Kill and Update buttons are active When there are no jobs currently running only the Monitor and Delete buttons are active These buttons act on the selected job By default only jobs started from the current project are shown To show other jobs choose All jobs or Active jobs only from the Show option menu When a job ends the results are incorporated into the project according to the settings used to launch the job The point at which the incorporation occurs depends on the preference set in the Jobs tab of the Preferences panel only when monitored the default when approved or automatically Jobs are incorporated only if they are part of the current project You can monitor jobs that are not part of the current project but their results are not incorporated To add their results to a project you must open the project and import the results Further information on job control including configuring your site monitoring jobs running jobs and job incorporation can be found in the Job Control Guide and the Installation Guide Gettin
Download Pdf Manuals
Related Search