TOPTOC

From PyMOLWiki
Revision as of 18:44, 28 October 2007 by Inchoate (talk | contribs) (PyMolWiki Top-Level Table Of Contents)
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Section Layout

Please see Discussion for more thoughts on the site organization.

PyMolWiki Top-Level Table Of Contents

  1. News
  2. Frequently Asked Questions
  3. Brag -- show off your best images or movies.
    1. News Discussion
    2. PyMol Beta
  4. Technical Issues
    1. Installation
      1. Linux
      2. MAC
      3. Windows
  5. Launching PyMOL
    1. Command Line Options
    2. 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. Cartoon
        4. Surface
        5. Mesh
        6. Spheres
        7. Dots
      5. Color
      6. Displaying biochemical properties
    3. Stereo 3D Display -- wrong place
      1. Linux XFree86 Configuration -- wrong place
    4. Scenes
    5. Mouse Settings
    6. Wizards
    7. Ray_Tracing
    8. Settings Reference
    9. Movies and Animations Topics
    10. Structure Alignment
    11. 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. 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
      2. Superimposition and RMSD
      3. NMR Restraints and Analysis
  12. Third Party Software
    1. PovRay
    2. Making_Movies Making Movies
    3. Codecs
    4. Surfaces and Voids
  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. Arbitrary_Graphics_Objects
  15. Uncategorized For new pages, misplaced pages, etc.

Tree 02:09, 16 Feb 2005 (CST)