BELGACOM maestro 2050 User Manual

Schrödinger PressMaestro User ManualMaestro 8.0User Manual

ContentsMaestro 8.0 User Manualx12.2.4 Setting Workspace Preferences... 18212.2.5 Set

Chapter 6: Displaying StructuresMaestro 8.0 User Manual84Figure 6.4. The Atoms tab of the Molecular Representation panel.6.2 Changing Molecular Repres

Chapter 6: Displaying StructuresMaestro 8.0 User Manual 856.2.1 Changing the Representation of AtomsIn the Atoms tab, you can choose between None, CPK

Chapter 6: Displaying StructuresMaestro 8.0 User Manual86Figure 6.5. The Bonds tab of the Molecular Representation panel.• Smoothing: You can smooth t

Chapter 6: Displaying StructuresMaestro 8.0 User Manual 87Figure 6.6. The Settings tab of the Molecular Representation panel.6.2.3 Changing Representa

Chapter 6: Displaying StructuresMaestro 8.0 User Manual88The seven slider controls have the following functions:• Wire Width (pixels)—adjust the width

Chapter 6: Displaying StructuresMaestro 8.0 User Manual 89Figure 6.7. The Ribbons tab of the Molecular Representation panel.With the exception of the

Chapter 6: Displaying StructuresMaestro 8.0 User Manual90Figure 6.8. The Ribbon options dialog box.You can apply the color schemes and the display opt

Chapter 6: Displaying StructuresMaestro 8.0 User Manual 91Figure 6.9. The Atom Labels panel.To open the Atom Labels panel, choose Atoms Labels from th

Chapter 6: Displaying StructuresMaestro 8.0 User Manual92Instead of choosing your own labels, you can choose from two fixed labeling schemes thatlabel

Chapter 6: Displaying StructuresMaestro 8.0 User Manual 93Figure 6.10. The Display/Undisplay Atoms panel.6.4.1 Selectively Displaying AtomsThe Display

ContentsMaestro 8.0 User Manual xiChapter 14: Printing and Saving Workspace Images... 20714.1 Printing an Image (File or P

Chapter 6: Displaying StructuresMaestro 8.0 User Manual94In the lower section, you can apply the operation to the following structural units using the

Chapter 7Maestro 8.0 User Manual 95Maestro User ManualChapter 7: Manipulating StructuresMaestro provides a range of tools for manipulating structures

Chapter 7: Manipulating StructuresMaestro 8.0 User Manual96The other operation that does not change the coordinates of the structure is zooming, which

Chapter 7: Manipulating StructuresMaestro 8.0 User Manual 97Figure 7.1. The Advanced Transformations panel.The controls for local transformations are

Chapter 7: Manipulating StructuresMaestro 8.0 User Manual987.2.1 Selecting Atoms for TransformationTo select the atoms that you want to move, use the

Chapter 8Maestro 8.0 User Manual 99Maestro User ManualChapter 8: ProjectsWhen you use Maestro, you are always working within a project. Projects are m

Chapter 8: ProjectsMaestro 8.0 User Manual100To open an existing project, choose Open from the Project menu, or click the Open a projecttoolbar button

Chapter 8: ProjectsMaestro 8.0 User Manual 101Figure 8.1. The Save Project As project selector.When a project is saved, all view transformations (tran

Chapter 8: ProjectsMaestro 8.0 User Manual102sions) are the only visible items. Most of the features of these panels are common to all opera-tions. Th

Chapter 8: ProjectsMaestro 8.0 User Manual 103You can edit the text in the annotation section, including the automatically generated text. Thestandard

ContentsMaestro 8.0 User ManualxiiC.7 Formal Charge Extensions ... 238C.8

Chapter 8: ProjectsMaestro 8.0 User Manual1048.2.1 Importing Structures From a FileWhen Maestro imports structures from a file, the structures are copi

Chapter 8: ProjectsMaestro 8.0 User Manual 1058.2.4 Merging Entries From Another ProjectYou can merge the entries from a specified project into the cur

Chapter 8: ProjectsMaestro 8.0 User Manual106Project entries have two states that represent how they are being used: the selection state andthe inclus

Chapter 8: ProjectsMaestro 8.0 User Manual 1078.3.2 The Project Table MenusThe menus on the Project Table menu bar are described briefly below. The use

Chapter 8: ProjectsMaestro 8.0 User Manual1088.3.3 Mouse Functions in the Project TableThe standard use of shift-click and control-click to select obj

Chapter 8: ProjectsMaestro 8.0 User Manual 1098.3.4 Project Table Shortcut MenusIn addition to the menus on the menu bar, the Project Table panel has

Chapter 8: ProjectsMaestro 8.0 User Manual110In addition to these shortcut menus, there are Surfaces and Hypotheses shortcut menus, whichare displayed

Chapter 8: ProjectsMaestro 8.0 User Manual 111Structure Only, and Both. The Hypotheses shortcut menu provides tools for display of Phasehypotheses. Th

Chapter 8: ProjectsMaestro 8.0 User Manual1128.3.5 Use of the Keyboard in the Project TableSome frequently used operations have been assigned shortcut

Chapter 8: ProjectsMaestro 8.0 User Manual 1138.3.6 Configuring the Project TableThe Project Table panel provides tools for controlling what is display

ContentsMaestro 8.0 User Manual xiiiAppendix F: Configuring the Maestro Menus ... 261Appendix G: Customiz

Chapter 8: ProjectsMaestro 8.0 User Manual114Header), or to a fixed width (Fixed Width), by choosing from the Columns button menu on thetoolbar, theCol

Chapter 8: ProjectsMaestro 8.0 User Manual 115Figure 8.3. The Find panel.If you click on the Project Table panel, then click Find Next, the search sta

Chapter 8: ProjectsMaestro 8.0 User Manual116Figure 8.4. The Entry Selection dialog box.8.4.1 The Select MenuThe Select menu provides tools for select

Chapter 8: ProjectsMaestro 8.0 User Manual 117Select menu. You can open the Entry Selection dialog box from the Select menu or using theSelect Only to

Chapter 8: ProjectsMaestro 8.0 User Manual118the default current entry selection isall.•Intersect limits the selection of entries to those in the curr

Chapter 8: ProjectsMaestro 8.0 User Manual 119To add entries from the Workspace to the current selection:1. Choose Add from the Select menu.2. Select

Chapter 8: ProjectsMaestro 8.0 User Manual120To rename multiple entries with the same name:1. Select the entries to be renamed.2. Click the entry name

Chapter 8: ProjectsMaestro 8.0 User Manual 121Figure 8.5. The Group By Entry Property panel.You can create an entry group by selecting entries, then c

Chapter 8: ProjectsMaestro 8.0 User Manual122• Step Size—Size of the bins used to divide the entries into groups. The bins includethe lower end of the

Chapter 8: ProjectsMaestro 8.0 User Manual 123Figure 8.6. The Move To Group dialog box.Entries that are inside a group can be moved out of the group o

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Chapter 8: ProjectsMaestro 8.0 User Manual124Figure 8.7. The Sort Project Table panel.To sort entries:1. Select the desired entries.2. Choose Entries

Chapter 8: ProjectsMaestro 8.0 User Manual 125To sort entry groups:1. Choose Groups from the Sort submenu of the Ta ble menuThe Sort Groups panel is

Chapter 8: ProjectsMaestro 8.0 User Manual1268.6 The ePlayerThe ePlayer allows you to view in succession the structures associated with selected entri

Chapter 8: ProjectsMaestro 8.0 User Manual 127Figure 8.9. The ePlayer Options panel.8.6.2 ePlayer OptionsThe ePlayer Options panel provides access to

Chapter 8: ProjectsMaestro 8.0 User Manual128its name in the Reference text box, or clicking the Choose button and choosing an entry fromthe list. The

Chapter 8: ProjectsMaestro 8.0 User Manual 129The View Poses submenu also allows you to turn on or off the display of H-bonds and contacts,to generate

Chapter 8: ProjectsMaestro 8.0 User Manual1308.8.1.2 Adding Properties by CopyingTo create a new property by copying an existing property, choose Copy

Chapter 8: ProjectsMaestro 8.0 User Manual 131Figure 8.11. The Calculate Properties panel.If you have previously calculated the property for some entr

Chapter 8: ProjectsMaestro 8.0 User Manual132Figure 8.12. The Project Table Calculator panel.• To add a constant to the formula, type the value in the

Chapter 8: ProjectsMaestro 8.0 User Manual 133Figure 8.13. The Copy Property panel.8.8.2 Editing PropertiesTo edit the contents of an individual Proje

Maestro 8.0 User Manual xvDocument ConventionsIn addition to the use of italics for names of documents, the font conventions that are used inthis docu

Chapter 8: ProjectsMaestro 8.0 User Manual134Figure 8.14. The Merge Properties panel.• If the destination property does not exist, it is created using

Chapter 8: ProjectsMaestro 8.0 User Manual 135Figure 8.15. The Rename Property panel and the Delete Property dialog box.To create a new property, sele

Chapter 8: ProjectsMaestro 8.0 User Manual136Figure 8.16. The Show Property dialog box.8.8.7 Displaying Selected PropertiesIf you want to limit the nu

Chapter 8: ProjectsMaestro 8.0 User Manual 1378.8.8 Moving and Resizing Property ColumnsYou can move and resize individual columns in the project tabl

Chapter 8: ProjectsMaestro 8.0 User Manual138If you want to discard all work done to a particular project during a Maestro session, you canrevert to t

Chapter 9Maestro 8.0 User Manual 139Maestro User ManualChapter 9: ToolsMaestro is equipped with tools for investigating and changing the properties of

Chapter 9: ToolsMaestro 8.0 User Manual140Figure 9.1. The Distances tab of the Measurements panel.To select atoms for measurement, select the Add mode

Chapter 9: ToolsMaestro 8.0 User Manual 141You can make measurements with the Measure distances, angles or dihedrals toolbar button.To make a measurem

Chapter 9: ToolsMaestro 8.0 User Manual142To see hydrogen bonds or contacts marked in the Workspace, select Display H-bonds or DisplayContacts. For co

Chapter 9: ToolsMaestro 8.0 User Manual 143You can also display hydrogen bonds from the toolbar. First, choose Inter H-bonds or Intra H-bonds from the

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Chapter 9: ToolsMaestro 8.0 User Manual1441. Use the Centroid panel to define a centroid atom.A dummy atom is placed at the mean position of the picked

Chapter 9: ToolsMaestro 8.0 User Manual 145Figure 9.4. The Superposition panel.If you want to compare more than two structures or if picking individua

Chapter 9: ToolsMaestro 8.0 User Manual146Workspace and clicking Selection, or by clicking Select and using the Atom Selectiondialog box to select the

Chapter 9: ToolsMaestro 8.0 User Manual 147Figure 9.5. The Sets panel.9.4 SetsSets are groups of atoms that can be used in a variety of Maestro operat

Chapter 9: ToolsMaestro 8.0 User Manual148If you select Show Markers, the atoms in the set are marked with green markers. If the markersobscure part o

Chapter 9: ToolsMaestro 8.0 User Manual 149Figure 9.6. The Protein Reports panel.9.5.3 Viewing Reports on Protein PropertiesReports on various propert

Chapter 9: ToolsMaestro 8.0 User Manual150Figure 9.7. The Ramachandran Plot panel.The plot area displays a plot of protein dihedrals for all residues

Chapter 9: ToolsMaestro 8.0 User Manual 151• Clicking on a point zooms the Workspace image in to that residue, and highlights it withpale yellow marke

Chapter 9: ToolsMaestro 8.0 User Manual1529.7 Visualization ToolsMaestro includes a range of visualization tools for various kinds of data—in addition

Chapter 10Maestro 8.0 User Manual 153Maestro User ManualChapter 10: PlottingMaestro’s Plot Facility allows you to generate XY plots of any two columns

Chapter 1Maestro 8.0 User Manual 1Maestro User ManualChapter 1: Maestro OverviewMaestro is the graphical user interface (GUI) for all of Schrödinger’s

Chapter 10: PlottingMaestro 8.0 User Manual154Figure 10.1. The New Plot dialog box.You can modify the appearance of the data point markers and the plo

Chapter 10: PlottingMaestro 8.0 User Manual 155Figure 10.2. The Plot XY panel.The zoom bar is the area at the right of the Plot XY panel. It contains

Chapter 10: PlottingMaestro 8.0 User Manual156As with entries in the Project Table, you can select plots and display plots independently.When you have

Chapter 10: PlottingMaestro 8.0 User Manual 157Figure 10.3. The Label Points dialog box.To label points, click the Label Points button, then click a d

Chapter 10: PlottingMaestro 8.0 User Manual158Figure 10.4. The Plot tab of the Plot Settings panel.10.3 Editing Plots and Plot SettingsThe Plot Settin

Chapter 10: PlottingMaestro 8.0 User Manual 159Modifying a Plot Caption: When you create a new plot, a caption is displayed underneath theplot in theP

Chapter 10: PlottingMaestro 8.0 User Manual160Figure 10.5. The Series tab of the Plot Settings panel.Making a Series the Project Table Selection: To r

Chapter 10: PlottingMaestro 8.0 User Manual 161Figure 10.6. The X Axis and Y Axis tabs of the Plot Settings panel.Creating an Additional Axis: To gene

Chapter 10: PlottingMaestro 8.0 User Manual16210.4 Updating Plots to Reflect Project Table ChangesIf the data values in the Project Table that are used

Chapter 11Maestro 8.0 User Manual 163Maestro User ManualChapter 11: SurfacesThe Maestro surface facility allows you to create and visualize molecular

Chapter 1: Maestro OverviewMaestro 8.0 User Manual2Most of the windows that are opened from Maestro are amodal, and are called panels. Morethan one pa

Chapter 11: SurfacesMaestro 8.0 User Manual164Atoms for surface displayThe surface is displayed only for the atoms specified in the Atoms For Surface D

Chapter 11: SurfacesMaestro 8.0 User Manual 165Probe radiusThis setting appears only on the Molecular Surface panel and the Extended Radius Surfacepan

Chapter 11: SurfacesMaestro 8.0 User Manual166Figure 11.1. The Molecular Surface panel.To open the Extended Radius Surface panel, choose Extended Radi

Chapter 11: SurfacesMaestro 8.0 User Manual 167Figure 11.3. The VDW Surface panel.11.1.4 van der Waals SurfacesThe VDW Surface panel is used to genera

Chapter 11: SurfacesMaestro 8.0 User Manual168Hydrophobic and hydrophilic regions are marked by surface contours that enclose the region.The “neither”

Chapter 11: SurfacesMaestro 8.0 User Manual 169that lie suitably close to the surface of the receptor but for which the water-dipole-orientingelectric

Chapter 11: SurfacesMaestro 8.0 User Manual170Select to open the Atom Selection dialog box and select atoms. Mapping box atoms must beassociated with

Chapter 11: SurfacesMaestro 8.0 User Manual 171If the job finishes while it is being monitored, the results are automatically incorporated andthe site

Chapter 11: SurfacesMaestro 8.0 User Manual172Figure 11.5. The Surface Table panel.You can create.visor.pltfiles using the Jaguar panel. When you run a

Chapter 11: SurfacesMaestro 8.0 User Manual 17311.4.1 Importing, Modifying, and Deleting SurfacesImporting surfacesTo import a.visor.pltfile from the S

Chapter 1: Maestro OverviewMaestro 8.0 User Manual 31.1.3 Keyboard ShortcutsMaestro supports keyboard shortcuts in some of its panels, including the m

Chapter 11: SurfacesMaestro 8.0 User Manual174Figure 11.6. The Limit panel.You can change the isovalue for a surface that has an associated volume: ei

Chapter 11: SurfacesMaestro 8.0 User Manual 175Figure 11.7. The Surface Table - Display Options dialog box.Style and TransparencySurfaces can be displ

Chapter 11: SurfacesMaestro 8.0 User Manual176Figure 11.8. Example of color ramp: electrostatic potential of benzene mapped to vander Waals surface.Wh

Chapter 12Maestro 8.0 User Manual 177Maestro User ManualChapter 12: Customizing MaestroMany aspects of the Maestro interface can be customized from wi

Chapter 12: Customizing MaestroMaestro 8.0 User Manual178location during a session and want to revert to the last saved layout, choose Restore SavedLa

Chapter 12: Customizing MaestroMaestro 8.0 User Manual 179Figure 12.1. The Project tab of the Preferences panel.Fit to screen when inclusion changesIn

Chapter 12: Customizing MaestroMaestro 8.0 User Manual180compressed version of the current state of the project. You can choose to keep or to remove t

Chapter 12: Customizing MaestroMaestro 8.0 User Manual 181Figure 12.2. The Directory tab of the Preferences panel.If you change the working directory

Chapter 12: Customizing MaestroMaestro 8.0 User Manual182Figure 12.3. The Label tab of the Preferences panel.• Display headings in labels: If you sele

Chapter 12: Customizing MaestroMaestro 8.0 User Manual 183fitting to screen. The duration of the animation can be controlled by entering a value in the

Copyright © 2007 Schrödinger, LLC. All rights reserved. CombiGlide, Epik, Glide,Impact, Jaguar, Liaison, LigPrep, Maestro, Phase, Prime, PrimeX, QikPr

Chapter 1: Maestro OverviewMaestro 8.0 User Manual4Figure 1.1. The Project Table panel.If you do not specify a project when you start Maestro, Maestro

Chapter 12: Customizing MaestroMaestro 8.0 User Manual184Figure 12.4. The Workspace tab of the Preferences panel.Figure 12.5. The Workspace Feedback p

Chapter 12: Customizing MaestroMaestro 8.0 User Manual 185Show workspace menu on right-click-and-holdSelect this option to display a shortcut (context

Chapter 12: Customizing MaestroMaestro 8.0 User Manual186Figure 12.6. The File Suffix tab of the Preferences panel.12.2.6 Setting Builder PreferencesIn

Chapter 12: Customizing MaestroMaestro 8.0 User Manual 187Allow united atom types while buildingThe use of united atom types can cause problems for us

Chapter 12: Customizing MaestroMaestro 8.0 User Manual188Figure 12.8. The Jobs tab of the Preferences panel.For job incorporation, there are three opt

Chapter 12: Customizing MaestroMaestro 8.0 User Manual 18912.3 Customizing ResourcesMaestro uses resource files to make settings for various parts of i

Chapter 12: Customizing MaestroMaestro 8.0 User Manual190You can also right-click on any of these controls or displays and choose Hide from the shortc

Chapter 12: Customizing MaestroMaestro 8.0 User Manual 191Figure 12.9. The Stereo and Perspective subtabs in the Display Options panel.12.5.2 Enabling

Chapter 12: Customizing MaestroMaestro 8.0 User Manual192labels using the Display fog on atom labels option. You can also turn fogging on or off with

Chapter 12: Customizing MaestroMaestro 8.0 User Manual 193Fog options are preserved between Maestro sessions.12.5.4 Depth CuesWhen you are viewing in

Chapter 1: Maestro OverviewMaestro 8.0 User Manual 51.4 Job Launching and IncorporationMaestro’s job launching and incorporation capabilities are desi

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Chapter 13Maestro 8.0 User Manual 195Maestro User ManualChapter 13: Scripting in MaestroMaestro provides several facilities for creating and using scr

Chapter 13: Scripting in MaestroMaestro 8.0 User Manual196To install a Python script:1. In the Manage Scripts panel, click Install Scripts.The Install

Chapter 13: Scripting in MaestroMaestro 8.0 User Manual 197To install a macro:1. Choose Manage from the Scripts menu.The Manage Scripts panel opens (s

Chapter 13: Scripting in MaestroMaestro 8.0 User Manual19813.1.3 Managing ScriptsIn addition to installing scripts and macros, the Manage Scripts pane

Chapter 13: Scripting in MaestroMaestro 8.0 User Manual 199and run your Python scripts directly from Maestro. For more information on the Scripts menu

Chapter 13: Scripting in MaestroMaestro 8.0 User Manual20013.3.1 Command HistoryBy default, most of the internal Maestro commands generated when you p

Chapter 13: Scripting in MaestroMaestro 8.0 User Manual 20113.3.4 Opening Existing Command ScriptsThe Command Script Editor panel provides two options

Chapter 13: Scripting in MaestroMaestro 8.0 User Manual2023. Choose a color in the By Palette tab, or select a color name in the By Name tab.To specif

Chapter 13: Scripting in MaestroMaestro 8.0 User Manual 20313.4 Creating Command AliasesIf you choose to use command scripts to perform operations in

Chapter 1: Maestro OverviewMaestro 8.0 User Manual6Some of these computational programs have additional capabilities:• Epik and LigPrep jobs can read

Chapter 13: Scripting in MaestroMaestro 8.0 User Manual204Figure 13.5. The Macros panel.13.5 Creating MacrosMaestro allows you to create two kinds of

Chapter 13: Scripting in MaestroMaestro 8.0 User Manual 205If the command input area is not visible, choose Command Input Area from the Display menu.1

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Chapter 14Maestro 8.0 User Manual 207Maestro User ManualChapter 14: Printing and Saving Workspace ImagesIn addition to creating Maestro, MacroModel, P

Chapter 14: Printing and Saving Workspace ImagesMaestro 8.0 User Manual208File FormatIf you selected Printer in the Print To section, only the Postscr

Chapter 14: Printing and Saving Workspace ImagesMaestro 8.0 User Manual 209Print CommandIf the UNIX shell you use requires a different print command f

Chapter 14: Printing and Saving Workspace ImagesMaestro 8.0 User Manual210The Save Image panel allows you to set the following options:• Format—choose

Chapter 14: Printing and Saving Workspace ImagesMaestro 8.0 User Manual 211• Image—Enter the desired width and height of the image. These proportions

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Chapter 15Maestro 8.0 User Manual 213Maestro User ManualChapter 15: HelpThis chapter describes the various ways in which you can obtain information on

Chapter 1: Maestro OverviewMaestro 8.0 User Manual 7StrikeStrike is intimately linked with the Project Facility, uses descriptor data from single or m

Chapter 15: HelpMaestro 8.0 User Manual214• Show Balloon Help—Display Balloon Help (tooltips) for interface components when thisitem is selected.15.2

Chapter 15: HelpMaestro 8.0 User Manual 215the topic is displayed. You can restrict the search to match the word exactly by selecting Matchwhole word,

Chapter 15: HelpMaestro 8.0 User Manual2162. Click Advanced Search Options at the bottom of the panel.3. UnderLook In, choose Select Index.4. Navigate

Chapter 15: HelpMaestro 8.0 User Manual 21715.6 Technical SupportIf you have questions that are not answered from any of the above sources, contact Sc

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Appendix AMaestro 8.0 User Manual 219Maestro User ManualAppendix A: The Maestro File FormatAll Schrödinger products use the Maestro file format as thei

Appendix A: The Maestro File FormatMaestro 8.0 User Manual220Blocks can be nested within other blocks, and if a block contains a list of data values,

Appendix A: The Maestro File FormatMaestro 8.0 User Manual 221A.3 Compressed FormatFiles may use a compressed format, most commonly when storing infor

Appendix A: The Maestro File FormatMaestro 8.0 User Manual222The first block in the file is unnamed. This contains required information that is relevant

Appendix A: The Maestro File FormatMaestro 8.0 User Manual 223 s_m_grow_nameThe name used by the Maestro structure builder. i_m_atomic_numberThe

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Appendix A: The Maestro File FormatMaestro 8.0 User Manual224 i_m_to_repThe graphical representation for the “to” half-bond. :::The end of the d

Appendix BMaestro 8.0 User Manual 225Maestro User ManualAppendix B: Atom TypesMaestro atom types are not “hard-wired” into the program, but are read i

Appendix B: Atom TypesMaestro 8.0 User Manual226Table B.1. Atom types and equivalents.No. Symbol DescriptionEquivalenciesMM2/MM3 Charmm Amber 1 C1 Car

Appendix B: Atom TypesMaestro 8.0 User Manual 22725 N2 Nitrogen - sp29 N, NR, NP,NH1, NH2N, NB, NC,N*, N226 N3 Nitrogen - sp38 NH3 NT27 NA United atom

Appendix B: Atom TypesMaestro 8.0 User Manual22851 SM S– (thiolate anion)52 S0 Any Sulfur S53 P3 Phosphorus, trivalent 25 P54 B2 Boron - sp22655 B3 Bo

Appendix B: Atom TypesMaestro 8.0 User Manual 22978 M7 Mn+779 f2 Fe+280 f3 Fe+381 o2 Co+282 o3 Co+383 n2 Ni+284 n3 Ni+385 c1 Cu+86 c2 Cu+287 Zn Zn+288

Appendix B: Atom TypesMaestro 8.0 User Manual230108 P0 Any phosphorus109 S4 Sulfur, tetravalent110 S6 Sulfur, hexavalent octahedral(e.g. SF6)111 P4 P+

Appendix B: Atom TypesMaestro 8.0 User Manual 231Table B.2. Generalized atom types.No. Symbol Description151 GA Isolated atom152 GB Linear-single coor

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Appendix CMaestro 8.0 User Manual 233Maestro User ManualAppendix C: Substructure NotationThis appendix describes a linear substructure notation propri

Chapter 2Maestro 8.0 User Manual 9Maestro User ManualChapter 2: The Maestro Main WindowThis chapter describes how to start and end a Maestro session,

Appendix C: Substructure NotationMaestro 8.0 User Manual234If there are multiple atom types for an element, a wildcard symbol encompassing all of thee

Appendix C: Substructure NotationMaestro 8.0 User Manual 235C0*C0-O0-C0-C0since*can match a single, double, or triple bond, this more generalized patt

Appendix C: Substructure NotationMaestro 8.0 User Manual236Arbitrarily deep nesting of branches is allowed.In patterns with more complex branching, th

Appendix C: Substructure NotationMaestro 8.0 User Manual 237C.6 ExamplesIn this section, some more complex examples are presented. The first is norborn

Appendix C: Substructure NotationMaestro 8.0 User Manual238N0=C0-C0=C0-C0=C0(-1)-C0=C0-C0=C0-5In this pattern, the atom types are general and the bond

Appendix C: Substructure NotationMaestro 8.0 User Manual 239It is possible to create paradoxical specifications:CP{-} — negatively charged CP (atom t

Appendix C: Substructure NotationMaestro 8.0 User Manual240C.9 Differences between mmsubs and bmin notationsFor the record, here are the known technic

Appendix DMaestro 8.0 User Manual 241Maestro User ManualAppendix D: UtilitiesSchrödinger software is distributed with a number of utility programs and

Appendix D: UtilitiesMaestro 8.0 User Manual242D.1.2 Conversions to and From Mol2 Formatmol2convertConvert structure files between Maestro and Sybyl Mo

Appendix D: UtilitiesMaestro 8.0 User Manual 243If the input file is not specified, input is taken from standard input. Likewise, if the output file isno

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual102.1.1 Starting Maestro on a Windows HostTo start Maestro, double-click the Maestro icon on

Appendix D: UtilitiesMaestro 8.0 User Manual244Conversion Behavior for Importing PDBWhere multiple atomic coordinates exist for a single PDB entry, Ma

Appendix D: UtilitiesMaestro 8.0 User Manual 245Using Templates for Non-Standard ResiduesThepdbconvertprogram has been supplied with connectivity and

Appendix D: UtilitiesMaestro 8.0 User Manual246Options:For multiple-n options, the right-most takes precedence.Example:$SCHRODINGER/utilities/sdconver

Appendix D: UtilitiesMaestro 8.0 User Manual 247Syntax:uniquesmiles [options]input-file output-filesOptions:D.2 Structure ExtractionThis section describ

Appendix D: UtilitiesMaestro 8.0 User Manual248Options:D.2.2 sdsubsetExtract a subset of structures from an SD format input file.Syntax:sdsubset -nrang

Appendix D: UtilitiesMaestro 8.0 User Manual 249Options:Filter conditions must be specified in the form “name op value”, or just name. Here, name isthe

Appendix D: UtilitiesMaestro 8.0 User Manual250Syntax:ligfilter [options]input-fileligfilter [-h] [-v]Options:Filter criteria must be specified in the f

Appendix D: UtilitiesMaestro 8.0 User Manual 251The list of functional groups that are defined by SMARTS patterns is extensive, and can befound in the

Appendix D: UtilitiesMaestro 8.0 User Manual252Options:Allowed treatment names:All-atom with Osp3/Nsp3-LpAll-atom with No-LpCsp3 United-atom with S-Lp

Appendix D: UtilitiesMaestro 8.0 User Manual 253D.5 Project ManagementThree utilities are available for project management,project_create, which creat

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual 112.2 The Main WindowThe Maestro main window is shown in Figure 2.1. The following main wind

Appendix D: UtilitiesMaestro 8.0 User Manual254Options:D.5.3 project_appendAppend the structures in the specified structure files to a project.Syntax:$S

Appendix D: UtilitiesMaestro 8.0 User Manual 255D.6 Unique Namesunique_namesThis program takes files in Maestro format and adjusts the numeric suffixes

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Appendix EMaestro 8.0 User Manual 257Maestro User ManualAppendix E: Customizing ColorsColors, color schemes, and color ramps are defined in resource fil

Appendix E: Customizing ColorsMaestro 8.0 User Manual258E.2 Color SchemesEach of the standard color schemes is defined in a separate file in theschemess

Appendix E: Customizing ColorsMaestro 8.0 User Manual 259This scheme first sets all atoms to white, then colors all the nitrogen atoms blue and the oxy

Appendix E: Customizing ColorsMaestro 8.0 User Manual260# Number of colors# 5# Color names for all colors of this color rampredorangeyellowgreenblueWh

Appendix FMaestro 8.0 User Manual 261Maestro User ManualAppendix F: Configuring the Maestro MenusThe items that appear on the menus on the Maestro main

Appendix F: Configuring the Maestro MenusMaestro 8.0 User Manual262Each item has an identifier. Separators are also included as items, and are numbered

Appendix GMaestro 8.0 User Manual 263Maestro User ManualAppendix G: Customizing the Online HelpThe files that are used in the Maestro online help syste

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual12Figure 2.1. The Maestro main window, showing all window components.The following main windo

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Maestro 8.0 User Manual 265Maestro User ManualGlossaryASD—Atom Selection dialog box.ASL—Atom Specification Language.button menu—The menu available from

GlossaryMaestro 8.0 User Manual266project—A collection of related data, such as structures with their associated properties. Theproject may include da

Maestro 8.0 User Manual 267IndexAactive atom, changing ... 52Add Property panel ...

Maestro 8.0 User Manual268Indexclipping planes ... 265and depth cues ...

Maestro 8.0 User Manual 269IndexEelectrostatic potential, displaying on asurface... 176element,

Maestro 8.0 User Manual270Indexfill volume, CPK representation... 88filters, entry ...

Maestro 8.0 User Manual 271Indexcoloring... 181displaying for hidden atoms ... 181

Maestro 8.0 User Manual272IndexOobject types ... 14, 71, 73online help...

Maestro 8.0 User Manual 273Indexclosing... 100converting to current version... 25

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual 13• Status bar—displays information about a particular atom, about structures in the Work-sp

Maestro 8.0 User Manual274Indexsearching for text... 114Select menu...

Maestro 8.0 User Manual 275IndexUuncompressing MacroModel files... 241undoingindividual operations ... 2

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Maestro 8.0 User Manual iiiContentsDocument Conventions...

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual14• Help—display various kinds of documentation, including online help, Balloon Help(tooltips

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual 15Workspace selection– Choose an object type for selecting– Open theAtom Selection dialog bo

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual16Tile entriesArrange entries in a rectangular grid in theWorkspace.Reset WorkspaceReset the

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual 172.5 The Status BarThe status bar displays information about the contents of the Workspace

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual18sequence viewer displays a label for the sequence, in the format row:pdbID_chainID, wherero

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual 192.7 Shortcut MenusSome of the main window components have shortcut menus, which you open b

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual20The differences in the selection shortcut menu between the Workspace and the sequenceviewer

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual 21RotamersOpen the Rotamers dialog box to select one of the standard rotamers for theselecte

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual222.8 Mouse FunctionsThe Workspace has special uses for the middle and right mouse buttons. T

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual 232.9 Shortcut KeysSome frequently used operations in the main window have been assigned sho

ContentsMaestro 8.0 User Manualiv2.11 Undoing Workspace Operations ... 272.11.1 U

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual242.10 Finding Objects in the WorkspaceIf you want to find an atom, molecule, residue, chain,

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual 25Figure 2.3. The Find Atoms panelMoleculeType the molecule number in the text box.ASLUse th

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual26Figure 2.4. The Workspace showing a found residue.Mark principal atomsA colored arrow (or c

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual 27step by entering a value in the Step size text box: for example, if you wanted to find ever

Chapter 2: The Maestro Main WindowMaestro 8.0 User Manual28To save an orientation:• Click the Save view button in the toolbar.To restore the saved ori

Chapter 3Maestro 8.0 User Manual 29Maestro User ManualChapter 3: Importing and Exporting Structures andDataThe primary place for reading and writing d

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual30Figure 3.1. The Import panel.3.1.1 Selecting FilesSelecting a file type:

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual 31PDB File dialog box, in which you can specify the four-letter PDB code

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual32On UNIX hosts you can use Babel from the command line to convert struct

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual 331. Choose PDB from the Format option menu.2. ClickGet PDB File.3. Ente

ContentsMaestro 8.0 User Manual v4.7.3 Adjusting the Stereochemistry ... 614.7.

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual34Creating groups: Structures can be added to the Project Table as single

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual 353.1.4 Entry Names for Imported StructuresThe names of entries in a pro

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual36Figure 3.2. The Jaguar Read File file selector.To read input files throug

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual 37Figure 3.3. The Export panel.To open the Export panel, choose Export S

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual38set in the File Suffix tab of the Preferences panel. Properties from the

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual 39File name + entry nameIf you choose File name + entry name, you must s

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual40combination-5.maeand a dialog box confirms that the files were written to

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual 41Selecting a directory: To select a directory, you can enter it in the

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual42Figure 3.5. The Import Spreadsheet panel.To import data, you must first

Chapter 3: Importing and Exporting Structures and DataMaestro 8.0 User Manual 43Figure 3.6. The Choose Import Key dialog box.To continue, choose the d

ContentsMaestro 8.0 User Manualvi6.4 Displaying and Undisplaying Atoms ... 926.4.1 Sel

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Chapter 4Maestro 8.0 User Manual 45Maestro User ManualChapter 4: Building and Adjusting StructuresMaestro provides a variety of tools for building and

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual46Draw structuresChoose an element for drawing structures freehand in the Workspace

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 474.2 Building a Structure From FragmentsWhenever possible, you should use fragmen

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual48metal undefined. To change the metal type, retype the center once it is placed in

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 49Figure 4.1. The Fragments tab of the Build panel, showing the Organic library.4.

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual50replace. If you click on a terminal atom, the fragment replaces the terminal atom

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 51To create a structure in Grow mode, click the fragments in the fragment library

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual52The basic operations of Draw mode are described below.• To begin drawing with the

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 53Figure 4.3. The Atom Properties tab showing tools for the Element property.4.4 C

ContentsMaestro 8.0 User Manual vii8.4 Selecting Project Entries ...

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual54If you want to change an atom to some other element, choose Element from the Prop

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 55• To decrease the formal charge, click the Decrement formal charge toolbar butto

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual56Figure 4.4. The Connect & Fuse panel.To delete an atom pair from the Connect

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 57• If you choose an existing entry other than the two source entries, the new str

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual58You can choose bond lengths or dihedrals for adjustment by right-clicking on a bo

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 59Figure 4.6. The Adjust panel, showing the Dihedral tab.4.7.2 Adjusting Peptide L

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual60The geometry of the converted link is only approximate, and should be refined befo

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 61Repeat steps 3 and 4 for each residue that you want to adjust. Note that no acco

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual62Figure 4.8. The Symmetrize Workspace panel.Structures that are built by drawing,

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 63Treatment section or click Select to open the Atom Selection dialog box and defin

ContentsMaestro 8.0 User Manualviii8.9 Undoing Project Operations... 137C

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual64Figure 4.9. The Hydrogen Treatment panel.4.9 Changing Atom PropertiesIn addition

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 65Figure 4.10. The Atom Type (MacroModel) tools in the Atom Properties tab.PDB Ato

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual66Figure 4.11. The PDB Atom Name tools in the Atom Properties tab.For some purposes

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 67Figure 4.12. The Atom Name tools in the Atom Properties tab.A canonical atom nam

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual68Figure 4.13. The Residue Number tools in the Residue Properties tab.4.10 Changing

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual 69Renumbering a single residue is the same as assigning its number. To apply a spe

Chapter 4: Building and Adjusting StructuresMaestro 8.0 User Manual70The centroid capability is available in the Centroids panel, which you open from

Chapter 5Maestro 8.0 User Manual 71Maestro User ManualChapter 5: Selecting AtomsMaestro has a powerful set of tools for selecting atoms in a structure

Chapter 5: Selecting AtomsMaestro 8.0 User Manual72• Selection button—Performs the action on any atoms already selected in the Workspace.•Previous but

Chapter 5: Selecting AtomsMaestro 8.0 User Manual 73Figure 5.2. The Sets panel, showing the Pick option menu.The Pick Option MenuWith the Pick option

ContentsMaestro 8.0 User Manual ix10.3 Editing Plots and Plot Settings... 15810.

Chapter 5: Selecting AtomsMaestro 8.0 User Manual74Figure 5.3. The Atom Selection dialog box.To open the Atom Selection dialog box, choose Select from

Chapter 5: Selecting AtomsMaestro 8.0 User Manual 75The features of the Atom Selection dialog box are described in the following sections.5.3.1 Select

Chapter 5: Selecting AtomsMaestro 8.0 User Manual765.3.3 Selecting Atoms Using Previously Defined Sets or SelectionsIn the Sets tab, you can select ato

Chapter 5: Selecting AtomsMaestro 8.0 User Manual 77Figure 5.4. The Proximity dialog box.• Previous—recall the atom selection defined the last time the

Chapter 5: Selecting AtomsMaestro 8.0 User Manual78You can also type ASL expressions directly into the ASL text box. The hand-edited expressionsare co

Chapter 5: Selecting AtomsMaestro 8.0 User Manual 796. Select the Sidechain option.7. ClickIntersect to restrict the current ASL expression to include

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Chapter 6Maestro 8.0 User Manual 81Maestro User ManualChapter 6: Displaying StructuresMaestro provides a wide selection of options for displaying stru

Chapter 6: Displaying StructuresMaestro 8.0 User Manual82Figure 6.1. The By Palette tab of the Atom Coloring panel.Figure 6.2. The By Name tab of the

Chapter 6: Displaying StructuresMaestro 8.0 User Manual 83Figure 6.3. The Color Scheme tab of the Atom Coloring panel.6.1.2 Using Predefined Schemes to