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VEGA Manual

1. Introduction

2. Running VEGA OpenGL

3. Mouse, keyboard
and joystick

4. The main menu

5. Editing
   5.1 Atoms
  
5.2 Atom properties
   5.3 Atom constraints
   5.4 Centroids
   5.5 Bonds
   5.6 Torsions
   5.7 Add a solvent cluster
   5.8 Add ions
   5.9 Build a solvent cluster
   5.10 Merge with another file
   5.11 The clipboard

6. Display
   6.1 Atom selection
   6.2 Display modes

   6.3 View settings
   6.4 Color
   6.5 Molecule information

7. Calculations
   7.1 Charges & Pot.

   7.2 Mopac
   7.3 Surface
   7.5 Trajectory analysis
   7.6 Selection Tool
   7.7 BioDock
   7.8 Interactions

8. Integrated Tools:
   8.1 GraphEd
   8.2 MiniEd
   8.3 Task Manager
   8.4 SendVegaCmd
   8.5 WinDD

9. Plugin system
   9.1 Introduction
   9.2 Dhrystone plugin
   9.3 Predator plugin
   9.4 ClustalX plugin
   9.5 PowerNet plugin
   9.6 REBOL
   9.7 Scripts
   9.8 Plugin SDK

10. Extended commands

11. Compatibility list