VIDA User Manual

Previous: Front Matter Up: VIDA User Manual Next: 1. Introduction

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Contents

• Front Matter
• 1. Introduction
  • 1.1 History
  • 1.2 OpenEye Toolkits
• 2. Installation
  • 2.1 Microsoft Windows
  • 2.2 UNIX/Linux
  • 2.3 Mac OS X
    • 2.3.1 Platform differences
    • 2.3.2 Launching from the command line
  • 2.4 Licenses
• 3. Getting Started
  • 3.1 General Concepts
    • 3.1.1 Focused State
    • 3.1.2 Visible State
    • 3.1.3 Locked State
    • 3.1.4 Marked State
    • 3.1.5 Selected State
  • 3.2 Scope
  • 3.3 Layout
    • 3.3.1 Main Windows
    • 3.3.2 Peripheral Windows
  • 3.4 Undo/Redo
• 4. File I/O
  • 4.1 Opening Files
    • 4.1.1 Molecules
    • 4.1.2 Grids
    • 4.1.3 Surfaces
    • 4.1.4 Python Scripts
    • 4.1.5 State
  • 4.2 Closing Files
  • 4.3 Saving Files
    • 4.3.1 Molecules
    • 4.3.2 Grids
    • 4.3.3 Surfaces
    • 4.3.4 State
  • 4.4 Importing Files
  • 4.5 Exporting Files
    • 4.5.1 Data
    • 4.5.2 Images
    • 4.5.3 Python
  • 4.6 Drag and Drop
• 5. 3D Display
  • 5.1 User Interaction
    • 5.1.1 Mouse
    • 5.1.2 Style Control
  • 5.2 Rendering
  • 5.3 Stereo
    • 5.3.1 Microsoft Windows
    • 5.3.2 Mac OS X
    • 5.3.3 UNIX/Linux
  • 5.4 Viewpoint
  • 5.5 Bookmarks
  • 5.6 Tiled Display
  • 5.7 Toolbars
    • 5.7.1 Style Toolbar
    • 5.7.2 Mouse Toolbar
    • 5.7.3 Application Toolbar
  • 5.8 Display Widgets
    • 5.8.1 Annotation
    • 5.8.2 Bookmark
    • 5.8.3 Data Display
    • 5.8.4 Depiction Widget
  • 5.9 Molecular Visualization
    • 5.9.1 Display Styles
    • 5.9.2 Color
    • 5.9.3 Proteins
    • 5.9.4 Monitors
    • 5.9.5 Hydrogen Bonds
  • 5.10 Grid Visualization
    • 5.10.1 Grid Types
    • 5.10.2 Reentrant Grids
  • 5.11 Surface Visualization
    • 5.11.1 Display Styles
    • 5.11.2 Color
    • 5.11.3 Selection
  • 5.12 Custom Views
    • 5.12.1 FRED View
    • 5.12.2 EON View
    • 5.12.3 ROCS View
• 6. 2D Display
  • 6.1 Preview vs. Viewer
  • 6.2 Interaction
• 7. Spreadsheet
  • 7.1 Basic Usage
  • 7.2 Sorting
  • 7.3 Displaying Data
  • 7.4 Organizing Columns
  • 7.5 Creating New Columns
    • 7.5.1 Math Functions
    • 7.5.2 OEChem Functions
  • 7.6 Filtering
  • 7.7 Statistics
  • 7.8 Formatting Columns
  • 7.9 Importing/Exporting
    • 7.9.1 Importing
    • 7.9.2 Exporting
• 8. List Management
  • 8.1 Introduction
  • 8.2 Browsing
  • 8.3 Views
  • 8.4 List Columns
  • 8.5 List Manipulation
    • 8.5.1 Creating Lists
    • 8.5.2 Deleting from Lists
  • 8.6 Toolbar
• 9. Process Management
  • 9.1 Processes
    • 9.1.1 Adding Input
    • 9.1.2 Adding Output
    • 9.1.3 Adding Prompts
  • 9.2 Pipes
• 10. Scripting
  • 10.1 Scripting Window
  • 10.2 OEChemLite
• 11. Preferences
• 12. Examples
  • 12.1 Data
  • 12.2 Scripts
• 13. Help
• A. Menus
  • A.1 File
    • A.1.1 Open
    • A.1.2 Open State
    • A.1.3 Open Special
    • A.1.4 Clear
    • A.1.5 Save
    • A.1.6 Save State
    • A.1.7 New List
    • A.1.8 New Molecule
    • A.1.9 Import
    • A.1.10 Export
    • A.1.11 Recents
    • A.1.12 Exit
  • A.2 Edit
    • A.2.1 Undo
    • A.2.2 Undo History
    • A.2.3 Redo
    • A.2.4 Redo History
    • A.2.5 Copy
    • A.2.6 Copy Image
    • A.2.7 Paste
    • A.2.8 Select
    • A.2.9 Mark
    • A.2.10 Hide
    • A.2.11 Find
    • A.2.12 Find on Disk
    • A.2.13 Preferences
  • A.3 View
    • A.3.1 Fullscreen
  • A.4 Data
    • A.4.1 Sort Spreadsheet
    • A.4.2 Filter Spreadsheet
    • A.4.3 Create Column
    • A.4.4 Format Columns
    • A.4.5 Organize Columns
    • A.4.6 Show Statistics
  • A.5 Style
    • A.5.1 Color
    • A.5.2 Selection
    • A.5.3 Display
    • A.5.4 Graphics
    • A.5.5 Symmetry
  • A.6 Bookmarks
    • A.6.1 Add
    • A.6.2 Organize
    • A.6.3 Animated
  • A.7 Tools
    • A.7.1 FRED View
    • A.7.2 EON View
    • A.7.3 ROCS View
  • A.8 Window
    • A.8.1 Main Window
    • A.8.2 2D Preview
    • A.8.3 2D Viewer
    • A.8.4 3D Viewer
    • A.8.5 List Window
    • A.8.6 Process Manager
    • A.8.7 Scripting Window
    • A.8.8 Spreadsheet
    • A.8.9 Style Control
  • A.9 Help
    • A.9.1 About
    • A.9.2 Dynamic Help
    • A.9.3 Documentation
    • A.9.4 Online Support
• B. Mouse Maps
  • B.1 VIDA Mouse Map
• C. Release Notes
  • C.1 Version 3.0.0
  • C.2 Version 2.1.2
  • C.3 Version 2.1.1
  • C.4 Version 2.1.0
  • C.5 Version 2.0.2
• Bibliography
• About this document ...

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				VIDA User Manual

Previous: Front Matter Up: VIDA User Manual Next: 1. Introduction

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Documentation released on 23 May 2007.