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TOPTOC

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Revision as of 06:27, 2 March 2005 by Tree (talk | contribs)
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Section Layout

Please see Discussion for more thoughts on the site organizaiton.

Layout Schema

  1. News
    1. Discussion
    2. PyMol Beta
  2. Technical Issues
    1. Installation
      1. OS Dependent
        1. Linux
        2. MAC
        3. Windows
  3. Launching PyMOL
    1. Command Line Options
    2. Launching From a Script
  4. 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
  5. Command Language
    1. PyMOL Command Script
    2. PyMOL Python API
  6. 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
  7. Scripting
    1. Example Scripts
    2. Script Library
  8. Plugins
    1. How to do electrostatics and energy minimization.
      1. APBS Plugin
    2. rtools
    3. Tutorial on writing plugins
    4. Others
  9. 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
  10. Third Party Software
    1. PovRay
    2. Movies
    3. Codecs
  11. Python Integration
  12. Unintended Uses (OpenGL Object Renderer)
    1. Arbitrary Graphics Objects
  13. Uncategorized For new pages, misplaced pages, etc.

Tree 02:09, 16 Feb 2005 (CST)

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