Maestro User Manual

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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