TOPTOC

Section Layout

Please see Discussion for more thoughts on the site organizaiton.

PyMolWiki Top-Level Table Of Contents

1. News
2. Frequently Asked Questions
3. Brag -- show off your best images or movies.
   1. Discussion
   2. PyMol Beta
4. Technical Issues
   1. Installation
      1. Linux
      2. MAC
      3. Windows
5. Launching PyMOL

• Command Line Options
• Launching From a Script

1. 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. Cartoon
         4. Surface
         5. Mesh
         6. Spheres
         7. Dots
      5. Color
      6. Displaying biochemical properties
   3. Display Settings
   4. Stereo 3D Display -- wrong place
      1. Hardware Options -- wrong place?
      2. Linux XFree86 Configuration -- wrong place
   5. Scenes
   6. Mouse Settings
   7. Wizards
   8. Ray_Tracing
   9. Settings Reference
   10. Movies and Animations
   11. Structure Alignment
   12. Structure Alignment Editor
2. Command Language
   1. PyMOL Command Script
   2. PyMOL Python API
3. 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
4. Scripting
   1. Example Scripts
   2. Script Library
5. Plugins
   1. How to do electrostatics and energy minimization.
      1. APBS Plugin
   2. rtools
   3. Tutorial on writing plugins
   4. Others
6. High-Level Applications
   1. Crystallography Applications
      1. Symmetry
      2. Electron Density
   2. NMR Applications
      1. Working with Structure Families
      2. Superimposition and RMSD
      3. NMR Restraints and Analysis
7. Third Party Software
   1. PovRay
   2. Movies
   3. Codecs
8. Python Integration
9. PyMol_Integration -- adding pymol to other projects (eg OpenGL Object Renderer)
   1. Nuccyl -- Nuccyl is a great PyMol extension
   2. Arbitrary_Graphics_Objects
10. Uncategorized For new pages, misplaced pages, etc.

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Tree 02:09, 16 Feb 2005 (CST)

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