TOPTOC

1. News
2. Frequently Asked Questions
3. Gallery -- PyMOL Gallery and HOWTO
4. Technical Issues
   1. Installation
      1. Linux
      2. MAC
      3. Windows
5. Launching
   1. Launching PyMOL
   2. Command Line Options
   3. Launching From a Script
6. Using PyMol
   1. Mouse Controls
   2. Objects and Selections
      1. Working with Objects
      2. Working with Selections
      3. Selector Quick Reference
         1. Single-word Selectors
         2. Property Selectors
         3. Selection Algebra
         4. Selection Macros
      4. Representations
         1. Lines
         2. Sticks
         3. Ball and Sticks
         4. Cartoon
         5. Surface
         6. Mesh
         7. Spheres
         8. Dots
   3. Coloring
      1. Color
   4. Biochemical Properties
      1. Displaying biochemical properties
   5. Stereo 3D Display -- wrong place
      1. Linux XFree86 Configuration -- wrong place
   6. Scenes
   7. Mouse Settings
   8. Wizards
   9. Ray_Tracing
   10. Settings Reference
   11. Movies and Animations Topics
   12. Structure Alignment'
   13. Structure Alignment Editor
7. PyMol Commands
8. Advanced Issues
   1. Modeling and editing structures
      1. Editing Atoms
      2. Molecular sculpting
      3. Homology modeling
   2. Image Manipulation
      1. Labels
      2. Photoshop/GIMP
      3. Stereo Figures
      4. Publication-quality images
9. Scripting
   1. Example Scripts
   2. Script Library
10. Plugins
    1. Electrostatics and energy minimization.
       1. APBS Plugin
       2. Protein_contact_potential
    2. rtools
    3. Tutorial on writing plugins
    4. Others
11. High-Level Applications
    1. Crystallography Applications
       1. Symmetry|Symmetry
       2. Electron Density
    2. NMR Applications
       1. Working with Structure Families
    3. Superimposition and RMSD
       1. NMR Restraints and Analysis
12. Third Party Software
    1. PovRay
    2. Making Movies
    3. Codecs
    4. Surfaces and Voids
    5. O
    6. SURFNET
13. Python Integration
14. PyMol_Integration -- adding pymol to other projects (eg OpenGL Object Renderer)
    1. Nuccyl -- Nuccyl is a great PyMol extension
    2. CASTp -- Binding and Active site prediction
    3. CCTBX -- Computational Crystallography Toolbox
    4. ProMOL
    5. S2S
    6. Arbitrary_Graphics_Objects
15. Uncategorized For new pages, misplaced pages, etc.