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Maestro User ManualMaestro 10.2User ManualSchrödinger Press
Maestro User Manual Copyright 2015 Schrödinger, LLC. All rights reserved.While care has been taken in the preparation of this publication, Schrödingerassumes no responsibility for errors or omissions, or for damages resulting fromthe use of the information contained herein.Canvas, CombiGlide, ConfGen, Epik, Glide, Impact, Jaguar, Liaison, LigPrep,Maestro, Phase, Prime, PrimeX, QikProp, QikFit, QikSim, QSite, SiteMap, Strike, andWaterMap are trademarks of Schrödinger, LLC. Schrödinger, BioLuminate, andMacroModel are registered trademarks of Schrödinger, LLC. MCPRO is a trademarkof William L. Jorgensen. DESMOND is a trademark of D. E. Shaw Research, LLC.Desmond is used with the permission of D. E. Shaw Research. All rights reserved.This publication may contain the trademarks of other companies.Schrödinger software includes software and libraries provided by third parties. Fordetails of the copyrights, and terms and conditions associated with such includedthird party software, use your browser to open third party legal.html, which is inthe docs folder of your Schrödinger software installation.This publication may refer to other third party software not included in or withSchrödinger software ("such other third party software"), and provide links to thirdparty Web sites ("linked sites"). References to such other third party software orlinked sites do not constitute an endorsement by Schrödinger, LLC or its affiliates.Use of such other third party software and linked sites may be subject to thirdparty license agreements and fees. Schrödinger, LLC and its affiliates have noresponsibility or liability, directly or indirectly, for such other third party softwareand linked sites, or for damage resulting from the use thereof. Any warranties thatwe make regarding Schrödinger products and services do not apply to such otherthird party software or linked sites, or to the interaction between, orinteroperability of, Schrödinger products and services and such other third partysoftware.May 2015
ContentsDocument Conventions . xixChapter 1: Maestro Overview . 11.1 General Interface Design . 11.1.1 Maestro Windows . 21.1.2 Mouse Functions. 21.1.3 Keyboard Shortcuts and Shortcut Menus . 31.1.4 File and Directory Selection . 31.2 Maestro Workflow . 51.3 Maestro Projects . 61.4 Access to Applications . 71.5 Running Jobs . 91.6 Citing Maestro in Publications . 10Chapter 2: The Maestro Main Window . 112.1 Starting Maestro . 112.1.1 Starting Maestro on a Windows Host. 112.1.2 Starting Maestro on a Mac Host . 122.1.3 Starting Maestro on a Linux Host . 122.1.4 Choosing a Profile. 132.2 The Main Window . 142.3 The Menu Bar . 162.4 The Main Window Toolbars . 172.4.1 The Project Toolbar. 202.4.2 The Edit Toolbar. 212.4.3 The Workspace Toolbar . 232.5 The Status Bar . 232.6 The Sequence Viewer . 252.7 Shortcut Menus . 26Maestro 10.2 User Manualiii
Contents2.8 Mouse Functions . 312.9 Shortcut Keys . 322.10 Finding Objects in the Workspace . 362.11 Undoing Workspace Operations . 372.12 Running Maestro Commands . 382.13 Ending a Maestro Session . 38Chapter 3: Importing and Exporting Structures and Data . 413.1 Importing Structures . 413.1.1 Selecting Files. 433.1.2 Selecting Import Settings. 463.1.3 Interacting with the Import Process . 483.1.4 Importing Structures from Another Project . 483.1.5 Importing Structures by Dragging onto the Workspace . 483.1.6 Importing Structures from the PDB Database . 483.1.7 Error Reporting for PDB Files . 493.1.8 Entry Names for Imported Structures . 513.1.9 Reading Jaguar Input Files . 513.2 Exporting Structures . 523.2.1 Selecting a File . 533.2.2 Selecting Export Settings. 543.2.3 Exporting Multiple Files. 553.3 Exporting Data to a Spreadsheet . 573.4 Importing Data From a Spreadsheet . 583.5 Exporting Structures and Data to a Canvas Project . 603.6 Exporting Data from a Table . 613.7 Copying and Pasting Structures . 61Chapter 4: Viewing the Workspace. 634.1 The View Toolbar . 63ivSchrödinger Software Release 2015-2
Contents4.2 Changing the View . 644.2.1 Translating the View . 654.2.2 Rotating the View . 654.2.3 Zooming In and Out . 664.2.4 Restoring the Default View. 674.2.5 Setting the View Origin and Rotation Center . 674.3 Saving, Restoring, and Managing Views . 674.4 Tiling the Workspace . 704.5 Using the Full Screen . 724.6 Clipping . 724.7 3D Viewing . 744.7.1 Stereo Viewing . 744.7.2 Using Perspective . 764.7.3 Using Fogging . 774.7.4 Depth Cues . 78Chapter 5: Building and Adjusting Structures . 795.1 The Build and Fragments Toolbars . 795.2 The Build Panel . 815.3 Building a Structure From Fragments . 825.3.1 Building Structures Using Place Mode. 845.3.2 Building Structures Using Grow Mode . 865.4 Building a Structure From Atoms . 875.5 Building a Structure in 2D . 895.5.1 The 2D Sketcher Menu Bar. 905.5.2 The 2D Sketcher Toolbar . 905.5.3 Sketching Molecules . 925.5.4 Saving Templates for Building. 945.5.5 Saving Structures. 945.6 Changing Elements . 95Maestro 10.2 User Manualv
Contents5.7 Changing the Bond Order and Formal Charge . 965.8 Connecting or Fusing Structures . 975.9 Adjusting the Geometry . 995.9.1 Adjusting Distances, Angles, and Dihedral Angles . 995.9.1.1 Using the Workspace Tools . 995.9.1.2 From the Adjust Panel . 1005.9.1.3 Repeating Adjustments . 1015.9.2 Adjusting Peptide Linkages and Side Chains . 1015.9.3 Adjusting the Stereochemistry . 1035.9.4 Adjusting Groups of Atoms . 1045.9.5 Structure Sculpting. 1075.9.6 Cleaning Up the Geometry . 1075.10 Adding and Treating Hydrogen Atoms . 1085.11 Changing Atom Properties . 1105.11.1 Atom type (MacroModel). 1105.11.2 Partial Charge . 1115.11.3 PDB Atom Name. 1115.11.4 Atom Name . 1125.11.5 Grow Name.
Maestro User Manual Copyright 2015 Schrödinger, LLC. All rights reserved. While care has been taken in the preparation of this publication, Schrödinger
