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 Maestro User Manual
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Document Outline - Maestro User Manual
- Contents
- Document Conventions
- Maestro Overview
- 1.1 General Interface Design
- 1.1.1 Maestro Windows
- 1.1.2 Mouse Functions
- 1.1.3 Keyboard Shortcuts and Shortcut Menus
- 1.1.4 File and Directory Selection
- 1.2 Maestro Workflow
- 1.3 Maestro Projects
- 1.4 Access to Applications
- 1.5 Running Jobs
- 1.6 Citing Maestro in Publications
- The Maestro Main Window
- 2.1 Starting Maestro
- 2.1.1 Starting Maestro on a Windows Host
- 2.1.2 Starting Maestro on a Mac Host
- 2.1.3 Starting Maestro on a Linux Host
- 2.1.4 Choosing a Profile
- 2.2 The Main Window
- 2.3 The Menu Bar
- 2.4 The Main Window Toolbars
- 2.4.1 The Project Toolbar
- 2.4.2 The Edit Toolbar
- 2.4.3 The Workspace Toolbar
- 2.5 The Status Bar
- 2.6 The Sequence Viewer
- 2.7 Shortcut Menus
- 2.8 Mouse Functions
- 2.9 Shortcut Keys
- 2.10 Finding Objects in the Workspace
- 2.11 Undoing Workspace Operations
- 2.12 Running Maestro Commands
- 2.13 Ending a Maestro Session
- Importing and Exporting Structures and Data
- 3.1 Importing Structures
- 3.1.1 Selecting Files
- 3.1.2 Selecting Import Settings
- 3.1.3 Interacting with the Import Process
- 3.1.4 Importing Structures from Another Project
- 3.1.5 Importing Structures by Dragging onto the Workspace
- 3.1.6 Importing Structures from the PDB Database
- 3.1.7 Error Reporting for PDB Files
- 3.1.8 Entry Names for Imported Structures
- 3.1.9 Reading Jaguar Input Files
- 3.2 Exporting Structures
- 3.2.1 Selecting a File
- 3.2.2 Selecting Export Settings
- 3.2.3 Exporting Multiple Files
- 3.3 Exporting Data to a Spreadsheet
- 3.4 Importing Data From a Spreadsheet
- 3.5 Exporting Structures and Data to a Canvas Project
- 3.6 Exporting Data from a Table
- 3.7 Copying and Pasting Structures
- Viewing the Workspace
- 4.1 The View Toolbar
- 4.2 Changing the View
- 4.2.1 Translating the View
- 4.2.2 Rotating the View
- 4.2.3 Zooming In and Out
- 4.2.4 Restoring the Default View
- 4.2.5 Setting the View Origin and Rotation Center
- 4.3 Saving, Restoring, and Managing Views
- 4.4 Tiling the Workspace
- 4.5 Using the Full Screen
- 4.6 Clipping
- 4.7 3D Viewing
- 4.7.1 Stereo Viewing
- 4.7.2 Using Perspective
- 4.7.3 Using Fogging
- 4.7.4 Depth Cues
- Building and Adjusting Structures
- 5.1 The Build and Fragments Toolbars
- 5.2 The Build Panel
- 5.3 Building a Structure From Fragments
- 5.3.1 Building Structures Using Place Mode
- 5.3.2 Building Structures Using Grow Mode
- 5.4 Building a Structure From Atoms
- 5.5 Building a Structure in 2D
- 5.5.1 The 2D Sketcher Menu Bar
- 5.5.2 The 2D Sketcher Toolbar
- 5.5.3 Sketching Molecules
- 5.5.4 Saving Templates for Building
- 5.5.5 Saving Structures
- 5.6 Changing Elements
- 5.7 Changing the Bond Order and Formal Charge
- 5.8 Connecting or Fusing Structures
- 5.9 Adjusting the Geometry
- 5.9.1 Adjusting Distances, Angles, and Dihedral Angles
- 5.9.1.1 Using the Workspace Tools
- 5.9.1.2 From the Adjust Panel
- 5.9.1.3 Repeating Adjustments
- 5.9.2 Adjusting Peptide Linkages and Side Chains
- 5.9.3 Adjusting the Stereochemistry
- 5.9.4 Adjusting Groups of Atoms
- 5.9.5 Structure Sculpting
- 5.9.6 Cleaning Up the Geometry
- 5.10 Adding and Treating Hydrogen Atoms
- 5.11 Changing Atom Properties
- 5.11.1 Atom type (MacroModel)
- 5.11.2 Partial Charge
- 5.11.3 PDB Atom Name
- 5.11.4 Atom Name
- 5.11.5 Grow Name
- 5.11.6 Isotope Number
- 5.11.7 Other Properties
- 5.12 Changing Residue Properties
- 5.13 Defining Dummy Atoms
- 5.14 Deleting Atoms and Bonds
- Selecting Atoms
- 6.1 Picking in the Workspace
- 6.2 Using the Toolbar Buttons
- 6.3 Using the Picking Tools
- 6.3.1 The Pick Option Menu
- 6.3.2 The Dihedral Selection Dialog Box
- 6.4 Using the Edit Menu
- 6.5 The Atom Selection Dialog Box
- 6.5.1 Selecting Atoms by Property
- 6.5.2 Selecting Atoms by Connectivity
- 6.5.3 Selecting Atoms Using Previously Defined Sets or Selections
- 6.5.4 Combining and Modifying Atom Selections
- 6.5.5 Selecting Atoms by Proximity
- 6.5.6 Editing and Storing Expressions
- 6.5.7 Converting Expressions to Lists
- 6.5.8 Examples of Atom Selection
- 6.6 Storing the Workspace Selection
- Changing the Appearance of Structures
- 7.1 The Representation Toolbar
- 7.2 Changing Atom, Bond, and Background Color
- 7.2.1 Applying a Single Color to Atoms and Bonds
- 7.2.2 Coloring Bonds by Atom Colors
- 7.2.3 Using Color Schemes to Color Atoms
- 7.2.4 Creating and Editing Color Schemes
- 7.2.5 Setting the Background Color
- 7.3 Changing Molecular Representations
- 7.3.1 Changing the Representation of Atoms And Bonds
- 7.3.2 Rendering Proteins, DNA, and RNA as Ribbons
- 7.4 Changing Lighting, Materials, and Special Effects
- 7.5 Displaying and Undisplaying Atoms
- 7.5.1 The Display Atoms Toolbar
- 7.5.2 Selectively Displaying Atoms
- 7.5.3 Displaying Periodic Structures
- 7.6 Display Styles
- 7.6.1 Applying the Workspace Style
- 7.6.2 Defining the Workspace Style
- 7.6.3 Surfaces
- Labeling and Annotating the Workspace
- 8.1 The Labels Toolbar
- 8.2 Labeling Atoms
- 8.3 Labeling Bonds
- 8.4 Captions
- 8.5 Highlights
- 8.5.1 Creating and Editing Highlights
- 8.5.2 Adding Text and an Arrow to a Highlight
- 8.5.3 Displaying Highlights
- 8.6 Displaying Entry Properties
- 8.7 Other Objects
- Projects
- 9.1 Project Operations
- 9.1.1 Creating and Opening Projects
- 9.1.2 Saving and Closing Projects
- 9.1.3 Backing Up Projects
- 9.1.4 Recovering Projects
- 9.1.5 Deleting Projects
- 9.1.6 Undoing Project Operations
- 9.1.7 The Project Selector Panels
- 9.1.8 The Project Summary Panel
- 9.2 Adding Entries to a Project
- 9.2.1 Importing Structures From a File
- 9.2.2 Creating Entries From Workspace Structures
- 9.2.3 Pasting Structures Into the Workspace
- 9.2.4 Incorporating Entries From Job Output
- 9.2.5 Merging Entries From Another Project
- 9.3 Using Scenes
- 9.4 The Project Table Panel
- 9.4.1 The Project Table Toolbars
- 9.4.1.1 Project Toolbar
- 9.4.1.2 Property Toolbar
- 9.4.2 The Project Table Menus
- 9.4.3 The Project Status Bar
- 9.4.4 Mouse Functions in the Project Table
- 9.4.5 Project Table Shortcut Menus
- 9.4.6 Use of the Keyboard in the Project Table
- 9.4.7 Configuring the Project Table
- 9.4.8 Navigating the Project Table
- 9.4.9 Finding and Replacing Text in the Project Table
- 9.5 Selecting Project Entries
- 9.5.1 The Select Menu
- 9.5.2 Selecting Entries By Property
- 9.5.3 Selecting Entries By Matching a SMARTS Pattern
- 9.5.4 Selecting Entries Using the Plot Panel
- 9.5.5 Selecting Entries Using the 2D Viewer Panel
- 9.5.6 Selecting Entries Randomly
- 9.5.7 Selecting Entries in Groups
- 9.5.8 Selection Examples
- 9.6 Operating on Entries
- 9.6.1 Including, Excluding, and Fixing Entries
- 9.6.2 Renaming Entries
- 9.6.3 Locking Entries
- 9.6.4 Duplicating Entries
- 9.6.5 Merging Multiple Entries
- 9.6.6 Copying and Pasting Entry Properties
- 9.6.7 Splitting Entries
- 9.6.8 Grouping Entries
- 9.6.9 Showing And Hiding Entries in Groups
- 9.6.10 Deleting Entries
- 9.6.11 Moving Entries
- 9.6.12 Sorting Entries and Entry Groups
- 9.6.13 Ranking and Sorting Entries by Rank
- 9.6.14 Recording a Movie from Selected Entries
- 9.7 The ePlayer
- 9.7.1 ePlayer Modes
- 9.7.2 ePlayer Options
- 9.8 Viewing Poses
- 9.9 Viewing 2D Structures
- 9.9.1 Displaying 2D Structures in the Project Table
- 9.9.2 The 2D Viewer Panel
- 9.10 The Entry List Panel
- 9.11 Entry Properties
- 9.11.1 The Stars and Mark Properties
- 9.11.2 The Date Added and Date Modified Properties
- 9.11.3 Creating New Properties
- 9.11.3.1 Adding Properties with a Default Value
- 9.11.3.2 Adding Properties by Copying
- 9.11.3.3 Calculating Properties from Structural Data
- 9.11.3.4 Calculating Properties from Other Properties
- 9.11.4 Editing Properties
- 9.11.5 Copying Properties
- 9.11.6 Merging Properties
- 9.11.7 Setting the Number of Decimals and the Notation for a Real Property
- 9.11.8 File Name Properties
- 9.11.9 Renaming Properties
- 9.11.10 Deleting Properties
- 9.11.11 Clearing Property Values
- 9.11.12 Showing and Hiding Properties
- 9.11.12.1 Using the Properties Menu
- 9.11.12.2 Using the Property Tree
- 9.11.13 Creating and Editing Custom Property Families
- 9.11.14 Coloring Table Cells By Property Value
- 9.11.15 Moving, Reordering, and Resizing Property Columns
- 9.11.16 Exporting and Importing Data
- Tools
- 10.1 Displaying Markers
- 10.2 Displaying Measurements in the Workspace
- 10.2.1 Measuring Distances, Angles, Dihedrals, and NMR Coupling
- 10.2.2 Displaying Nonbonded Interactions
- 10.2.3 Displaying H-H NMR Coupling Constants
- 10.2.4 Storing the Results of Measurements
- 10.2.5 Defining Dummy Atoms for Measurements
- 10.2.6 Positioning and Formatting Measurement Labels
- 10.3 Superimposing and Aligning Structures
- 10.3.1 The Superposition Panel
- 10.3.2 The Flexible Ligand Alignment Panel
- 10.3.3 Aligning Centers of Mass
- 10.3.4 Aligning Proteins
- 10.4 Using Atom Sets
- 10.4.1 Creating and Deleting Sets
- 10.4.2 Selecting Atoms for a Set
- 10.4.3 Reading and Writing Sets
- 10.4.4 Selecting Atoms in the Workspace that Match a Set
- 10.5 Ligand Analysis Tools
- 10.5.1 R-Group Analysis
- 10.5.2 Scaffold Decomposition
- 10.6 Protein Tools
- 10.6.1 Assigning Protein Secondary Structure
- 10.6.2 Viewing Reports on Protein Properties
- 10.6.3 Protein Reliability Reports
- 10.6.4 Ramachandran Plots
- 10.6.5 Energy Profiles of Torsional and Rotamer States
- 10.6.6 Ligand Interaction Diagrams
- 10.6.7 Protein Splicing
- 10.6.8 The Multiple Sequence Viewer
- 10.7 Assigning Bond Orders and Partial Charges
- 10.8 Ligand Filtering
- 10.8.1 Selecting a Structure Source
- 10.8.2 Defining the Matching Method
- 10.8.3 Defining Matching Criteria
- 10.8.4 Defining New Matching Patterns
- 10.8.5 Eliminating Duplicate Ligands
- 10.9 Minimizing Structures
- Plotting
- 11.1 Scatter Plots
- 11.1.1 Managing Plots
- 11.1.2 Creating Plots
- 11.1.3 Changing Plot Settings
- 11.1.3.1 Changing the Plotted Properties
- 11.1.3.2 Changing the Plot Symbols and Lines
- 11.1.3.3 Changing the Axis and Color Scale Settings
- 11.1.3.4 Changing the Plot Shape and Area
- 11.1.3.5 Adding a Title and a Legend
- 11.1.3.6 Labeling Plot Points
- 11.1.4 Changing the View of a Plot
- 11.1.5 Interacting with the Project Table
- 11.1.6 Saving Plot Images
- 11.2 Plotting Coordinate Scan Results
- 11.2.1 General Features of Coordinate Scan Plot Panels
- 11.2.2 The Plot of One-Coordinate Scan Panel
- 11.2.3 The Plot of Two-Coordinate Scan Panel
- Surfaces
- 12.1 Generating Surfaces
- 12.1.1 Surface Generation Controls
- 12.1.2 Molecular Surfaces
- 12.1.3 Extended Radius Surfaces
- 12.1.4 Van der Waals Surfaces
- 12.1.5 Electrostatic Potential Surfaces
- 12.2 Hydrophobic/philic Surfaces
- 12.2.1 Background
- 12.2.2 Mapping Algorithm
- 12.2.3 Specifying a Structure to Be Mapped
- 12.2.4 Defining the Mapping Box
- 12.2.5 Running the Job
- 12.2.6 Viewing the Surface
- 12.3 Importing Surface or Volume Files
- 12.4 The Manage Surfaces Panel
- 12.4.1 Importing, Modifying, and Deleting Surfaces
- 12.4.2 Changing the Appearance of the Surface
- 12.4.2.1 Style and Transparency
- 12.4.2.2 Color Scheme
- 12.4.2.3 Depth Perception
- 12.4.3 Displaying Volumes
- 12.4.4 Exporting Surfaces
- Customizing Maestro
- 13.1 Changing and Saving Panel Layout
- 13.2 Customizing the Menus and Keyboard Shortcuts
- 13.3 Customizing Mouse Actions
- 13.4 Customizing Profiles
- 13.5 Customization by Editing Resource Files
- 13.5.1 Visual Style Resources
- 13.5.2 Color Definitions
- 13.5.3 Color Schemes
- 13.5.3.1 The scheme.res File
- 13.5.3.2 Color Scheme Files
- 13.5.4 Color Ramps
- 13.5.4.1 The ramp.res File
- 13.5.4.2 Color Ramp Files
- 13.5.5 Column Data in the Project Table
- 13.5.6 Property Families
- 13.5.7 Maestro Menus
- 13.5.8 Rotamers
- Setting Preferences
- 14.1 General Preferences
- 14.1.1 History
- 14.1.2 Directories
- 14.1.3 File extensions
- 14.1.4 Appearance
- 14.1.5 Application Fonts
- 14.1.6 Panels
- 14.1.7 Quitting Maestro
- 14.2 Project Preferences
- 14.2.1 Opening and Closing Projects
- 14.2.2 Backups
- 14.2.3 Entry Changes
- 14.2.4 Importing Structures
- 14.3 Project Table Preferences
- 14.3.1 Properties
- 14.3.2 Colors
- 14.3.3 Groups
- 14.4 Workspace Preferences
- 14.4.1 Picking
- 14.4.2 View Animation
- 14.4.3 Translation
- 14.4.4 Rotation
- 14.4.5 Trackpad
- 14.4.6 Transformations
- 14.4.7 Dipole Moment
- 14.4.8 Clipping Planes
- 14.4.9 Fonts
- 14.4.10 Fitting
- 14.4.11 Zooming
- 14.4.12 Depth View
- 14.4.13 Changes
- 14.4.14 Periodicity
- 14.4.15 Crystal Mates
- 14.4.16 Graphics
- 14.4.17 Sequence Viewer
- 14.4.18 Display/Undisplay Atoms
- 14.5 Feedback Preferences
- 14.5.1 Atom
- 14.5.2 Properties
- 14.5.3 Job
- 14.6 Atom/Bond Labels Preferences
- 14.7 Measurements Preferences
- 14.8 Non-Bonded Interactions Preferences
- 14.8.1 Criteria
- 14.8.1.1 H-Bonds
- 14.8.1.2 Halogen bonds
- 14.8.1.3 Contacts
- 14.8.2 Display
- 14.9 Surfaces Preferences
- 14.9.1 Creation
- 14.9.2 Viewing
- 14.9.3 Performance
- 14.12.1 Behavior
- 14.12.2 Geometry cleanup
- 14.13.1 Starting
- 14.13.2 Monitoring
- 14.13.3 Incorporation
- 14.13.4 Directory
- 14.14.1 Atoms and Bonds
- 14.14.2 Ribbons
- Scripting in Maestro
- 15.1 The Scripts Menu
- 15.2 Using Python and Python Scripts
- 15.3 Scripting and KNIME Workflows
- 15.4 Using Command Scripts
- 15.4.1 Command History
- 15.4.2 Building a Command Script
- 15.4.3 Saving a Command Script
- 15.4.4 Opening Existing Command Scripts
- 15.4.5 Running and Stopping Scripts
- 15.4.6 Copying Commands as Python Commands
- 15.4.7 Customizations You Can Perform With a Script
- 15.5 Creating Command Aliases
- 15.6 Creating Macros
- 15.6.1 Named Macros
- 15.6.2 Function Key Macros
- Saving Workspace Images
- 16.1 Saving Images to a File
- 16.2 Copying Images to Other Applications
- Using Maestro with Other Applications
- 17.1 Canvas
- 17.2 KNIME
- 17.3 PyMOL
- 17.4 ChemDraw and ISIS/Draw
- Help
- 18.1 The Help Menu
- 18.2 Maestro Help
- 18.3 Context-Sensitive Help
- 18.4 Manuals
- 18.5 Tutorials
- 18.6 The Schrödinger Web Site
- 18.7 Technical Support
- The Maestro File Format
- A.1 Basic File Description
- A.2 Data Blocks
- A.3 Compressed Format
- A.4 Data Item Names
- A.5 Example Maestro File
- Atom Types
- Substructure Notation
- C.1 Atom and Bond Types
- C.2 Ring closure
- C.3 Chain branching
- C.4 Optional atoms
- C.5 Special Cases
- C.6 Examples
- C.7 Formal Charge Extensions
- C.8 Atom Type Equivalence Labels
- C.9 Differences between mmsubs and bmin notations
- C.10 Related Files
- Project Utilities
- D.1 project_convert
- D.2 project_create
- D.3 project_append
- D.4 project_extract
- D.5 project_version
- Property Names
- Glossary
- Index
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