Maestro User Manual

[Pages:478]Maestro User Manual

Maestro 10.2

User Manual

Schr?dinger Press

Maestro 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 herein.

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May 2015

Contents

Document Conventions ................................................................................................... xix

Chapter 1: Maestro Overview ........................................................................................ 1

1.1 General Interface Design ......................................................................................... 1 1.1.1 Maestro Windows ............................................................................................... 2 1.1.2 Mouse Functions................................................................................................. 2 1.1.3 Keyboard Shortcuts and Shortcut Menus ........................................................... 3 1.1.4 File and Directory Selection ................................................................................ 3

1.2 Maestro Workflow ..................................................................................................... 5 1.3 Maestro Projects........................................................................................................ 6 1.4 Access to Applications ............................................................................................ 7 1.5 Running Jobs............................................................................................................. 9 1.6 Citing Maestro in Publications.............................................................................. 10

Chapter 2: The Maestro Main Window.................................................................. 11

2.1 Starting Maestro ...................................................................................................... 11 2.1.1 Starting Maestro on a Windows Host................................................................ 11 2.1.2 Starting Maestro on a Mac Host ....................................................................... 12 2.1.3 Starting Maestro on a Linux Host ..................................................................... 12 2.1.4 Choosing a Profile............................................................................................. 13

2.2 The Main Window .................................................................................................... 14 2.3 The Menu Bar ........................................................................................................... 16 2.4 The Main Window Toolbars ................................................................................... 17

2.4.1 The Project Toolbar........................................................................................... 20 2.4.2 The Edit Toolbar................................................................................................ 21 2.4.3 The Workspace Toolbar .................................................................................... 23 2.5 The Status Bar ......................................................................................................... 23 2.6 The Sequence Viewer ............................................................................................. 25 2.7 Shortcut Menus ....................................................................................................... 26

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2.8 Mouse Functions ..................................................................................................... 31 2.9 Shortcut Keys .......................................................................................................... 32 2.10 Finding Objects in the Workspace ..................................................................... 36 2.11 Undoing Workspace Operations ........................................................................ 37 2.12 Running Maestro Commands ............................................................................. 38 2.13 Ending a Maestro Session................................................................................... 38

Chapter 3: Importing and Exporting Structures and Data ....................... 41

3.1 Importing Structures .............................................................................................. 41 3.1.1 Selecting Files................................................................................................... 43 3.1.2 Selecting Import Settings.................................................................................. 46 3.1.3 Interacting with the Import Process .................................................................. 48 3.1.4 Importing Structures from Another Project ....................................................... 48 3.1.5 Importing Structures by Dragging onto the Workspace .................................... 48 3.1.6 Importing Structures from the PDB Database .................................................. 48 3.1.7 Error Reporting for PDB Files ........................................................................... 49 3.1.8 Entry Names for Imported Structures ............................................................... 51 3.1.9 Reading Jaguar Input Files ............................................................................... 51

3.2 Exporting Structures .............................................................................................. 52 3.2.1 Selecting a File ................................................................................................. 53 3.2.2 Selecting Export Settings.................................................................................. 54 3.2.3 Exporting Multiple Files..................................................................................... 55

3.3 Exporting Data to a Spreadsheet ......................................................................... 57 3.4 Importing Data From a Spreadsheet.................................................................... 58 3.5 Exporting Structures and Data to a Canvas Project ......................................... 60 3.6 Exporting Data from a Table.................................................................................. 61 3.7 Copying and Pasting Structures .......................................................................... 61

Chapter 4: Viewing the Workspace.......................................................................... 63

4.1 The View Toolbar ..................................................................................................... 63

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4.2 Changing the View .................................................................................................. 64 4.2.1 Translating the View .......................................................................................... 65 4.2.2 Rotating the View .............................................................................................. 65 4.2.3 Zooming In and Out .......................................................................................... 66 4.2.4 Restoring the Default View................................................................................ 67 4.2.5 Setting the View Origin and Rotation Center .................................................... 67

4.3 Saving, Restoring, and Managing Views ............................................................ 67 4.4 Tiling the Workspace .............................................................................................. 70 4.5 Using the Full Screen ............................................................................................. 72 4.6 Clipping ..................................................................................................................... 72 4.7 3D Viewing ................................................................................................................ 74

4.7.1 Stereo Viewing .................................................................................................. 74 4.7.2 Using Perspective ............................................................................................. 76 4.7.3 Using Fogging ................................................................................................... 77 4.7.4 Depth Cues ....................................................................................................... 78

Chapter 5: Building and Adjusting Structures................................................... 79

5.1 The Build and Fragments Toolbars...................................................................... 79 5.2 The Build Panel........................................................................................................ 81 5.3 Building a Structure From Fragments................................................................. 82

5.3.1 Building Structures Using Place Mode.............................................................. 84 5.3.2 Building Structures Using Grow Mode .............................................................. 86 5.4 Building a Structure From Atoms ........................................................................ 87 5.5 Building a Structure in 2D ..................................................................................... 89 5.5.1 The 2D Sketcher Menu Bar............................................................................... 90 5.5.2 The 2D Sketcher Toolbar .................................................................................. 90 5.5.3 Sketching Molecules ......................................................................................... 92 5.5.4 Saving Templates for Building........................................................................... 94 5.5.5 Saving Structures.............................................................................................. 94 5.6 Changing Elements................................................................................................. 95

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5.7 Changing the Bond Order and Formal Charge .................................................. 96

5.8 Connecting or Fusing Structures......................................................................... 97

5.9 Adjusting the Geometry ......................................................................................... 99 5.9.1 Adjusting Distances, Angles, and Dihedral Angles ........................................... 99 5.9.1.1 Using the Workspace Tools .................................................................... 99 5.9.1.2 From the Adjust Panel .......................................................................... 100 5.9.1.3 Repeating Adjustments ........................................................................ 101 5.9.2 Adjusting Peptide Linkages and Side Chains ................................................. 101 5.9.3 Adjusting the Stereochemistry ........................................................................ 103 5.9.4 Adjusting Groups of Atoms ............................................................................. 104 5.9.5 Structure Sculpting.......................................................................................... 107 5.9.6 Cleaning Up the Geometry ............................................................................. 107

5.10 Adding and Treating Hydrogen Atoms............................................................ 108

5.11 Changing Atom Properties ................................................................................ 110 5.11.1 Atom type (MacroModel)............................................................................... 110 5.11.2 Partial Charge ............................................................................................... 111 5.11.3 PDB Atom Name........................................................................................... 111 5.11.4 Atom Name ................................................................................................... 112 5.11.5 Grow Name................................................................................................... 113 5.11.6 Isotope Number ............................................................................................ 113 5.11.7 Other Properties ........................................................................................... 114

5.12 Changing Residue Properties........................................................................... 115

5.13 Defining Dummy Atoms ..................................................................................... 117

5.14 Deleting Atoms and Bonds ............................................................................... 117

Chapter 6: Selecting Atoms ........................................................................................ 119

6.1 Picking in the Workspace .................................................................................... 119

6.2 Using the Toolbar Buttons................................................................................... 119

6.3 Using the Picking Tools ....................................................................................... 121 6.3.1 The Pick Option Menu .................................................................................... 123 6.3.2 The Dihedral Selection Dialog Box ................................................................. 124

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6.4 Using the Edit Menu.............................................................................................. 125

6.5 The Atom Selection Dialog Box.......................................................................... 125 6.5.1 Selecting Atoms by Property........................................................................... 126 6.5.2 Selecting Atoms by Connectivity..................................................................... 127 6.5.3 Selecting Atoms Using Previously Defined Sets or Selections ....................... 127 6.5.4 Combining and Modifying Atom Selections .................................................... 127 6.5.5 Selecting Atoms by Proximity.......................................................................... 128 6.5.6 Editing and Storing Expressions ..................................................................... 129 6.5.7 Converting Expressions to Lists...................................................................... 129 6.5.8 Examples of Atom Selection ........................................................................... 130

6.6 Storing the Workspace Selection ....................................................................... 131

Chapter 7: Changing the Appearance of Structures.................................. 133

7.1 The Representation Toolbar ................................................................................ 133

7.2 Changing Atom, Bond, and Background Color ............................................... 134 7.2.1 Applying a Single Color to Atoms and Bonds ................................................. 134 7.2.2 Coloring Bonds by Atom Colors...................................................................... 135 7.2.3 Using Color Schemes to Color Atoms ............................................................ 135 7.2.4 Creating and Editing Color Schemes.............................................................. 138 7.2.5 Setting the Background Color ......................................................................... 141

7.3 Changing Molecular Representations ............................................................... 141 7.3.1 Changing the Representation of Atoms And Bonds ....................................... 141 7.3.2 Rendering Proteins, DNA, and RNA as Ribbons ............................................ 143

7.4 Changing Lighting, Materials, and Special Effects ......................................... 145

7.5 Displaying and Undisplaying Atoms ................................................................. 150 7.5.1 The Display Atoms Toolbar ............................................................................. 150 7.5.2 Selectively Displaying Atoms .......................................................................... 150 7.5.3 Displaying Periodic Structures ........................................................................ 152

7.6 Display Styles ........................................................................................................ 154 7.6.1 Applying the Workspace Style ........................................................................ 155 7.6.2 Defining the Workspace Style ......................................................................... 156

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7.6.3 Surfaces .......................................................................................................... 159

Chapter 8: Labeling and Annotating the Workspace................................. 161

8.1 The Labels Toolbar................................................................................................ 161 8.2 Labeling Atoms...................................................................................................... 162 8.3 Labeling Bonds...................................................................................................... 166 8.4 Captions .................................................................................................................. 167 8.5 Highlights................................................................................................................ 168

8.5.1 Creating and Editing Highlights....................................................................... 169 8.5.2 Adding Text and an Arrow to a Highlight ......................................................... 170 8.5.3 Displaying Highlights....................................................................................... 170 8.6 Displaying Entry Properties ................................................................................ 171 8.7 Other Objects ......................................................................................................... 171

Chapter 9: Projects............................................................................................................ 173

9.1 Project Operations ................................................................................................ 173 9.1.1 Creating and Opening Projects....................................................................... 173 9.1.2 Saving and Closing Projects ........................................................................... 174 9.1.3 Backing Up Projects........................................................................................ 176 9.1.4 Recovering Projects ........................................................................................ 176 9.1.5 Deleting Projects............................................................................................. 177 9.1.6 Undoing Project Operations............................................................................ 177 9.1.7 The Project Selector Panels............................................................................ 177 9.1.8 The Project Summary Panel ........................................................................... 178

9.2 Adding Entries to a Project ................................................................................. 179 9.2.1 Importing Structures From a File .................................................................... 179 9.2.2 Creating Entries From Workspace Structures................................................. 179 9.2.3 Pasting Structures Into the Workspace........................................................... 180 9.2.4 Incorporating Entries From Job Output........................................................... 180 9.2.5 Merging Entries From Another Project............................................................ 180

9.3 Using Scenes ......................................................................................................... 181

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