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 Toolbars
    • 3.3.2 Main Windows
    • 3.3.3 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 Data
    • 4.1.6 State
  • 4.2 Closing Files
  • 4.3 Saving Files
    • 4.3.1 Molecules
    • 4.3.2 State
  • 4.4 Exporting Files
    • 4.4.1 Data
    • 4.4.2 Images
  • 4.5 Drag and Drop
• 5. 3D Display
  • 5.1 User Interaction
    • 5.1.1 Rotation
    • 5.1.2 Translation
    • 5.1.3 Scale/Zoom
    • 5.1.4 Clipping
    • 5.1.5 Depth Cue
    • 5.1.6 Selection
    • 5.1.7 Label
    • 5.1.8 Menu
  • 5.2 Rendering
  • 5.3 Stereo
  • 5.4 Viewpoint
  • 5.5 Tiled Display
  • 5.6 Visualization Toolbar
  • 5.7 Molecular Visualization
    • 5.7.1 Display Styles
    • 5.7.2 Selection
    • 5.7.3 Color
    • 5.7.4 Proteins
    • 5.7.5 Monitors
    • 5.7.6 Hydrogen Bonds
    • 5.7.7 Style Toolbar
  • 5.8 Grid Visualization
    • 5.8.1 Predefined Types
    • 5.8.2 Reentrant Grids
    • 5.8.3 Contour Resolution
    • 5.8.4 Contour Toolbar
  • 5.9 Surface Visualization
    • 5.9.1 Display Styles
    • 5.9.2 Color
    • 5.9.3 Transparency
    • 5.9.4 Selection
  • 5.10 Annotation
  • 5.11 Custom Views
    • 5.11.1 Docking View
    • 5.11.2 EON View
    • 5.11.3 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 Creating New Columns
    • 7.4.1 Math Functions
    • 7.4.2 OEChem Functions
  • 7.5 Filtering
  • 7.6 Statistics
  • 7.7 Importing/Exporting
• 8. Form Browser
  • 8.1 Export Display to HTML
• 9. List Management
  • 9.1 Introduction
  • 9.2 Browsing
  • 9.3 List Columns
  • 9.4 List Manipulation
    • 9.4.1 Creating Lists
    • 9.4.2 Deleting from Lists
  • 9.5 List Toolbar
• 10. Process Management
  • 10.1 Processes
    • 10.1.1 Adding Input
    • 10.1.2 Adding Output
    • 10.1.3 Adding Prompts
  • 10.2 Pipes
• 11. Scripting
  • 11.1 Scripting Window
  • 11.2 Command Browser
  • 11.3 OEChemLite
• 12. Preferences
• 13. Examples
  • 13.1 Data
  • 13.2 Scripts
• A. Release Notes
  • A.1 VIDA
• 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 26 July 2006.