TOPTOC: Difference between revisions

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# [[:Category:Using Pymol|Using PyMol]]
# [[:Category:Using Pymol|Using PyMol]]
## [[:Category:Mouse Controls|Mouse Controls]]
## [[:Category:Mouse Controls|Mouse Controls]]
## [[:Category:Objects and Selections|Objects and Selections]]
## [[Objects and Selections|Objects and Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
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#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
### [[Displaying Biochemical Properties|Displaying biochemical properties]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place

Revision as of 09:35, 6 May 2005

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. OS Dependent
        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. 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
  7. Command Language
    1. PyMOL Command Script
    2. PyMOL Python API
  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. How to do 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
      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. Movies
    3. Codecs
  13. Python Integration
  14. PyMol_Integration -- adding pymol to other projects (eg OpenGL Object Renderer)
    1. Nuccyl -- Nuccyl is a great PyMol extension
    2. Arbitrary_Graphics_Objects
  15. Uncategorized For new pages, misplaced pages, etc.

Tree 02:09, 16 Feb 2005 (CST)

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