Transcription of Maestro User Manual
1 Schr dinger PressMaestro User ManualMaestro User ManualMaestro User Manual Copyright 2015 Schr dinger, LLC. All rights reserved. While care has been taken in the preparation of this publication, Schr dinger assumes no responsibility for errors or omissions, or for damages resulting from the use of the information contained , CombiGlide, ConfGen, Epik, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro , Phase, Prime, PrimeX, QikProp, QikFit, QikSim, QSite, SiteMap, Strike, and WaterMap are trademarks of Schr dinger, LLC. Schr dinger, BioLuminate, and MacroModel are registered trademarks of Schr dinger, LLC. MCPRO is a trademark of 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 dinger software includes software and libraries provided by third parties. For details of the copyrights, and terms and conditions associated with such included third party software, use your browser to open , which is in the docs folder of your Schr dinger software publication may refer to other third party software not included in or with Schr dinger software ("such other third party software"), and provide links to third party Web sites ("linked sites").
2 References to such other third party software or linked sites do not constitute an endorsement by Schr dinger, LLC or its affiliates. Use of such other third party software and linked sites 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 such other third party software and linked sites, or for damage resulting from the use thereof. Any warranties that we make regarding Schr dinger products and services do not apply to such other third party software or linked sites, or to the interaction between, or interoperability of, Schr dinger products and services and such other third party 2015 Maestro User ManualiiiContentsDocument xixChapter 1: Maestro General Interface Maestro Windows .. Mouse Keyboard Shortcuts and Shortcut Menus .. File and Directory Selection .. Maestro Workflow .. Maestro Access to Running Citing Maestro in 10 Chapter 2: The Maestro Main Starting Starting Maestro on a Windows Starting Maestro on a Mac Host.
3 Starting Maestro on a Linux Host .. Choosing a The Main The Menu The Main Window The Project Toolbar .. The Edit Toolbar .. The Workspace Toolbar .. The Status The Sequence Shortcut 26 ContentsSchr dinger Software Release Mouse Shortcut Finding Objects in the Undoing Workspace Running Maestro Ending a Maestro 38 Chapter 3: Importing and Exporting Structures and Importing Selecting Selecting Import Settings .. Interacting with the Import Process .. Importing Structures from Another Project .. Importing Structures by Dragging onto the Workspace .. Importing Structures from the PDB Database .. Error Reporting for PDB Files .. Entry Names for Imported Structures .. Reading Jaguar Input Files .. Exporting Selecting a File .. Selecting Export Exporting Multiple Exporting Data to a Importing Data From a Exporting Structures and Data to a Canvas Exporting Data from a Copying and Pasting 61 Chapter 4: Viewing the The View 63 ContentsMaestro User Changing the Translating the View.
4 Rotating the View .. Zooming In and Out .. Restoring the Default Setting the View Origin and Rotation Center .. Saving, Restoring, and Managing Tiling the Using the Full 3D Stereo Viewing .. Using Perspective .. Using Fogging .. Depth Cues .. 78 Chapter 5: Building and Adjusting The Build and Fragments The Build Building a Structure From Building Structures Using Place Building Structures Using Grow Mode .. Building a Structure From Building a Structure in The 2D Sketcher Menu The 2D Sketcher Toolbar .. Sketching Molecules .. Saving Templates for Building .. Saving Changing 95 ContentsSchr dinger Software Release Changing the Bond Order and Formal Connecting or Fusing Adjusting the Adjusting Distances, Angles, and Dihedral Angles .. Using the Workspace From the Adjust Repeating Adjusting Peptide Linkages and Side Chains .. Adjusting the Stereochemistry.
5 Adjusting Groups of Atoms .. Structure Cleaning Up the Geometry .. Adding and Treating Hydrogen Changing Atom Atom type (MacroModel).. Partial Charge .. PDB Atom Atom Name .. Grow Name .. Isotope Number .. Other Properties .. Changing Residue Defining Dummy Deleting Atoms and 117 Chapter 6: Selecting Picking in the Using the Toolbar Using the Picking The Pick Option Menu .. The Dihedral Selection Dialog Box .. 124 ContentsMaestro User Using the Edit The Atom Selection Dialog Selecting Atoms by Selecting Atoms by Selecting Atoms Using Previously Defined Sets or Selections .. Combining and Modifying Atom Selections .. Selecting Atoms by Editing and Storing Expressions .. Converting Expressions to Examples of Atom Selection .. Storing the Workspace 131 Chapter 7: Changing the Appearance of The Representation Changing Atom, Bond, and Background Applying a Single Color to Atoms and Bonds.
6 Coloring Bonds by Atom Colors .. Using Color Schemes to Color Atoms .. Creating and Editing Color Schemes .. Setting the Background Color .. Changing Molecular Changing the Representation of Atoms And Bonds .. Rendering Proteins, DNA, and RNA as Ribbons .. Changing Lighting, Materials, and Special Displaying and Undisplaying The Display Atoms Toolbar .. Selectively Displaying Atoms .. Displaying Periodic Structures .. Display Applying the Workspace Style .. Defining the Workspace Style .. 156 ContentsSchr dinger Software Release Surfaces .. 159 Chapter 8: Labeling and Annotating the The Labels Labeling Labeling Creating and Editing Adding Text and an Arrow to a Highlight .. Displaying Displaying Entry Other 171 Chapter 9: Project Creating and Opening Saving and Closing Projects .. Backing Up Recovering Projects .. Deleting Undoing Project Operations.
7 The Project Selector The Project Summary Panel .. Adding Entries to a Importing Structures From a File .. Creating Entries From Workspace Pasting Structures Into the Incorporating Entries From Job Output .. Merging Entries From Another Using 181 ContentsMaestro User The Project Table The Project Table Project Property The Project Table Menus .. The Project Status Mouse Functions in the Project Table .. Project Table Shortcut Menus .. Use of the Keyboard in the Project Table .. Configuring the Project Table .. Navigating the Project Table .. Finding and Replacing Text in the Project Table .. Selecting Project The Select Menu .. Selecting Entries By Property .. Selecting Entries By Matching a SMARTS Selecting Entries Using the Plot Panel .. Selecting Entries Using the 2D Viewer Panel .. Selecting Entries Selecting Entries in Groups .. Selection Examples .. Operating on Including, Excluding, and Fixing Entries.
8 Renaming Entries .. Locking Entries .. Duplicating Entries .. Merging Multiple Entries .. Copying and Pasting Entry Properties .. Splitting Entries .. Grouping Entries .. Showing And Hiding Entries in Groups .. Deleting Moving Entries .. Sorting Entries and Entry Groups .. 211 ContentsSchr dinger Software Release Ranking and Sorting Entries by Rank .. Recording a Movie from Selected The ePlayer Modes .. ePlayer Viewing Viewing 2D Displaying 2D Structures in the Project Table .. The 2D Viewer Panel .. The Entry List Entry The Stars and Mark The Date Added and Date Modified Properties .. Creating New Adding Properties with a Default Adding Properties by Calculating Properties from Structural Calculating Properties from Other Editing Properties .. Copying Properties .. Merging Properties .. Setting the Number of Decimals and the Notation for a Real File Name Properties.
9 Renaming Properties .. Deleting Properties .. Clearing Property Values .. Showing and Hiding Properties .. Using the Properties Using the Property Creating and Editing Custom Property Families .. Coloring Table Cells By Property Value .. Moving, Reordering, and Resizing Property Columns .. Exporting and Importing Data .. 248 ContentsMaestro User ManualxiChapter 10: Displaying Displaying Measurements in the Measuring Distances, Angles, Dihedrals, and NMR Coupling .. Displaying Nonbonded Interactions .. Displaying H-H NMR Coupling Storing the Results of Defining Dummy Atoms for Measurements .. Positioning and Formatting Measurement Labels .. Superimposing and Aligning The Superposition The Flexible Ligand Alignment Aligning Centers of Mass .. Aligning Proteins .. Using Atom Creating and Deleting Sets .. Selecting Atoms for a Reading and Writing Sets .. Selecting Atoms in the Workspace that Match a Set.
10 Ligand Analysis R-Group Analysis .. Scaffold Decomposition .. Protein Assigning Protein Secondary Structure .. Viewing Reports on Protein Properties .. Protein Reliability Reports .. Ramachandran Plots .. Energy Profiles of Torsional and Rotamer States .. Ligand Interaction Diagrams .. Protein Splicing .. The Multiple Sequence Viewer .. 278 ContentsSchr dinger Software Release Assigning Bond Orders and Partial Ligand Selecting a Structure Source .. Defining the Matching Method .. Defining Matching Criteria .. Defining New Matching Eliminating Duplicate Minimizing Visualization 284 Chapter 11: Scatter Managing Plots .. Creating Plots .. Changing Plot Settings .. Changing the Plotted Changing the Plot Symbols and Changing the Axis and Color Scale Changing the Plot Shape and Adding a Title and a Labeling Plot Changing the View of a Interacting with the Project Table.
