Schrödinger 6.5 Maestro software User Manual
Maestro 6.5 is a graphical user interface for all of Schrödinger’s computational programs: FirstDiscovery (Glide, Impact, Liaison, QSite), Jaguar, LigPrep, MacroModel, Prime, and QikProp. It contains tools for building, displaying, and manipulating chemical structures; for organizing, loading and storing these structures and associated data; and for setting up, submitting, monitoring, and visualizing the results of calculations on these structures.
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User Manual
Maestro 6.5
Maestro 6.5
Copyright © 2004 Schrödinger, LLC. All rights reserved.
Schrödinger, FirstDiscovery, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Prime, QikProp, and
QSite are trademarks of Schrödinger, LLC.
MacroModel is a registered trademark of Schrödinger, LLC.
To the maximum extent permitted by applicable law, this publication is provided “as is” without
warranty of any kind. This publication may contain trademarks of other companies.
Revision A, June 2004
Schrödinger, FirstDiscovery, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Prime, QikProp, and
QSite are trademarks of Schrödinger, LLC.
MacroModel is a registered trademark of Schrödinger, LLC.
To the maximum extent permitted by applicable law, this publication is provided “as is” without
warranty of any kind. This publication may contain trademarks of other companies.
Revision A, June 2004
Maestro 6.5 User Manual iii
Contents
Chapter 1: Document Overview..........................................................................1
Chapter 2: Maestro Overview .............................................................................3
2.1 Starting Maestro...................................................................................................3
2.2 General Interface Design .....................................................................................4
2.2.1 Maestro Windows.....................................................................................5
2.2.2 Mouse Functions ......................................................................................5
2.3 The Maestro Main Window .................................................................................6
2.3.1 The Toolbar .............................................................................................7
2.3.2 Shortcut Keys .........................................................................................10
2.4 Maestro Workflow .............................................................................................11
2.5 Maestro Projects ................................................................................................11
2.6 Job Launching and Incorporation ......................................................................12
2.7 Undoing Workspace Operations ........................................................................14
2.7.1 Undoing Operations on the Structures ...................................................14
2.7.2 Undoing Operations on the View ...........................................................15
2.8 Ending a Maestro Session..................................................................................15
Chapter 3: Importing and Exporting Structures and Data............................17
3.1 Importing Structures ..........................................................................................17
3.1.1 Selecting Files ........................................................................................18
3.1.2 Selecting Import Settings .......................................................................20
3.1.3 Error Reporting for PDB Files ...............................................................21
3.1.4 Entry Naming Conventions for Imported Structures .............................22
3.1.5 Reading Jaguar Input Files.....................................................................22
3.2 Exporting Structures ..........................................................................................23
3.2.1 Selecting Export Settings .......................................................................24
3.2.2 Exporting Multiple Files ........................................................................25
3.3 Exporting Data to a Spreadsheet........................................................................26
3.4 Importing Data from a Spreadsheet ...................................................................28
Chapter 4: Building Structures.........................................................................31
4.1 The Build Panel..................................................................................................31
4.2 Building a Structure From Fragments ...............................................................32
4.2.1 Building Structures Using Place Mode ..................................................34
4.2.2 Building Structures Using Grow Mode..................................................36
Contents
Chapter 1: Document Overview..........................................................................1
Chapter 2: Maestro Overview .............................................................................3
2.1 Starting Maestro...................................................................................................3
2.2 General Interface Design .....................................................................................4
2.2.1 Maestro Windows.....................................................................................5
2.2.2 Mouse Functions ......................................................................................5
2.3 The Maestro Main Window .................................................................................6
2.3.1 The Toolbar .............................................................................................7
2.3.2 Shortcut Keys .........................................................................................10
2.4 Maestro Workflow .............................................................................................11
2.5 Maestro Projects ................................................................................................11
2.6 Job Launching and Incorporation ......................................................................12
2.7 Undoing Workspace Operations ........................................................................14
2.7.1 Undoing Operations on the Structures ...................................................14
2.7.2 Undoing Operations on the View ...........................................................15
2.8 Ending a Maestro Session..................................................................................15
Chapter 3: Importing and Exporting Structures and Data............................17
3.1 Importing Structures ..........................................................................................17
3.1.1 Selecting Files ........................................................................................18
3.1.2 Selecting Import Settings .......................................................................20
3.1.3 Error Reporting for PDB Files ...............................................................21
3.1.4 Entry Naming Conventions for Imported Structures .............................22
3.1.5 Reading Jaguar Input Files.....................................................................22
3.2 Exporting Structures ..........................................................................................23
3.2.1 Selecting Export Settings .......................................................................24
3.2.2 Exporting Multiple Files ........................................................................25
3.3 Exporting Data to a Spreadsheet........................................................................26
3.4 Importing Data from a Spreadsheet ...................................................................28
Chapter 4: Building Structures.........................................................................31
4.1 The Build Panel..................................................................................................31
4.2 Building a Structure From Fragments ...............................................................32
4.2.1 Building Structures Using Place Mode ..................................................34
4.2.2 Building Structures Using Grow Mode..................................................36
Contents
iv Maestro 6.5 User Manual
4.3 Building a Structure From Atoms......................................................................36
4.4 Changing Elements ............................................................................................38
4.5 Changing the Bond Order and Formal Charge ..................................................39
4.6 Fusing or Connecting Structures........................................................................40
4.7 Adjusting the Geometry.....................................................................................42
4.8 Applying a Hydrogen Treatment .......................................................................43
4.9 Changing Atom Properties.................................................................................45
4.10 Changing Residue Properties...........................................................................49
4.11 Defining Dummy Atoms..................................................................................50
4.12 Deleting Atoms ................................................................................................51
Chapter 5: Selecting Atoms ...............................................................................53
5.1 The Pick Menu...................................................................................................53
5.2 The Atom Selection Dialog Box........................................................................54
5.2.1 Selecting Atoms by Property .................................................................55
5.2.2 Combining and Modifying Atom Selections .........................................56
5.2.3 Selecting Atoms by Proximity ...............................................................56
5.2.4 Editing and Storing Expressions ............................................................57
5.2.5 Examples of Atom Selection..................................................................57
Chapter 6: Displaying Structures......................................................................59
6.1 Changing Atom Color........................................................................................59
6.1.1 Applying a Single Color.........................................................................59
6.1.2 Using Predefined Schemes to Color Atoms ...........................................61
6.2 Changing Molecular Representations ................................................................61
6.2.1 Changing the Representation of Atoms .................................................61
6.2.2 Changing the Representation of Bonds..................................................62
6.2.3 Changing Representation Attributes ......................................................64
6.2.4 Rendering Proteins as Ribbons ..............................................................65
6.3 Labeling Atoms..................................................................................................67
6.4 Displaying and Undisplaying Atoms.................................................................69
Chapter 7: Manipulating Structures.................................................................71
7.1 Global Transformations .....................................................................................71
7.2 Local Transformations .......................................................................................72
7.2.1 Selecting Atoms for Transformation......................................................73
7.2.2 Selecting a Rotation Center....................................................................74
7.3 Tiling Multiple Entries.......................................................................................74
iv Maestro 6.5 User Manual
4.3 Building a Structure From Atoms......................................................................36
4.4 Changing Elements ............................................................................................38
4.5 Changing the Bond Order and Formal Charge ..................................................39
4.6 Fusing or Connecting Structures........................................................................40
4.7 Adjusting the Geometry.....................................................................................42
4.8 Applying a Hydrogen Treatment .......................................................................43
4.9 Changing Atom Properties.................................................................................45
4.10 Changing Residue Properties...........................................................................49
4.11 Defining Dummy Atoms..................................................................................50
4.12 Deleting Atoms ................................................................................................51
Chapter 5: Selecting Atoms ...............................................................................53
5.1 The Pick Menu...................................................................................................53
5.2 The Atom Selection Dialog Box........................................................................54
5.2.1 Selecting Atoms by Property .................................................................55
5.2.2 Combining and Modifying Atom Selections .........................................56
5.2.3 Selecting Atoms by Proximity ...............................................................56
5.2.4 Editing and Storing Expressions ............................................................57
5.2.5 Examples of Atom Selection..................................................................57
Chapter 6: Displaying Structures......................................................................59
6.1 Changing Atom Color........................................................................................59
6.1.1 Applying a Single Color.........................................................................59
6.1.2 Using Predefined Schemes to Color Atoms ...........................................61
6.2 Changing Molecular Representations ................................................................61
6.2.1 Changing the Representation of Atoms .................................................61
6.2.2 Changing the Representation of Bonds..................................................62
6.2.3 Changing Representation Attributes ......................................................64
6.2.4 Rendering Proteins as Ribbons ..............................................................65
6.3 Labeling Atoms..................................................................................................67
6.4 Displaying and Undisplaying Atoms.................................................................69
Chapter 7: Manipulating Structures.................................................................71
7.1 Global Transformations .....................................................................................71
7.2 Local Transformations .......................................................................................72
7.2.1 Selecting Atoms for Transformation......................................................73
7.2.2 Selecting a Rotation Center....................................................................74
7.3 Tiling Multiple Entries.......................................................................................74
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Key Features
- Graphical user interface
- Building, displaying, manipulating chemical structures
- Organizing, loading and storing structures and data
- Setting up, submitting, monitoring and visualizing calculations
Related manuals
Frequently Answers and Questions
What is Maestro 6.5 used for?
Maestro 6.5 is a graphical user interface for all of Schrödinger’s computational programs, including FirstDiscovery, Jaguar, LigPrep, MacroModel, Prime, and QikProp. It allows users to build, display, and manipulate chemical structures, organize and store data, and set up, submit, monitor, and visualize calculations.
What are some of the key features of Maestro 6.5?
Maestro 6.5 offers a wide range of features, including tools for building, displaying, and manipulating chemical structures, organizing and storing data, setting up and submitting calculations, monitoring job progress, and visualizing the results.
How do I start a Maestro 6.5 session?
To start Maestro 6.5, you need to set the SCHRODINGER environment variable to point to the installation directory and potentially set the DISPLAY environment variable if it is not set automatically. Then, you can start Maestro using the command: '$SCHRODINGER/maestro [options] [filename]'.
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