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PyMol Wiki Home

You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.


If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

  • A wiki edit/user policy is needed.
  • Wiki schema/design/organization: Below you'll find the current layout design
  • Graphic design and CSS layout: We need logos, BG images and CSS layout
  • Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
  • Etc...

Editors Needed

If you feel you have the time to help import data into the PyMol wiki, please email Tree.

We need your help. So join today & happy editing!


Section Layout

Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.

Please see Discussion for more thoughts on the site organizaiton.

Layout Schema

    1. Discussion
    2. The Bleeding Edge
  1. Technical Issues (installation, hardware)
    1. Installation
      1. OS Dependent
        1. Linux
        2. MAC
        3. Windows
  2. Using the GUI
    1. Launching PyMOL
      1. Command Line Options
      2. Launching From a Script
    2. Mouse Controls
    3. 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
    4. Display Settings
    5. Stereo 3D Display
      1. Hardware Options
      2. Linux XFree86 Configuration
    6. Scenes
    7. Mouse Settings
    8. Wizards
    9. Plugins
    10. Ray-tracing
    11. Settings Reference (all settings and what they do)
    12. Movies and Animations
    13. Structure Alignment
    14. Structure Alignment Editor
  3. Command Language (I added a sample category. Should we continue with something like this?) Charlie
    1. PyMOL Command Script
    2. PyMOL Python API
  4. Advanced Issues (Ray tracing, settings)
    1. Launching PyMOL (has been asked often)
    2. Advanced Atom Selections
    3. Modeling and editing structures.
      1. Editing atoms
      2. Molecular sculpting
      3. Homology modeling
    4. Image Manipulation
      1. labels
      2. Photoshop/GIMP
      3. Stereo Figures
      4. Creating publication-quality images HOWTO
  5. Scripting
    1. Example Scripts
    2. Script Library
  6. Plugins
    1. List of Plugins
    2. How to do electrostatics and energy minimization.
      1. APBS Plugin
    3. rtools Plugin
    4. Tutorial on writing plugins
    5. Others
  7. High-level applications (Crystallography, NMR)
    1. Crystallography Applications
      1. Symmetry
      2. Electron Density
    2. NMR Applications
      1. Working with a Family of Structures
      2. Superimposition and RMSD
      3. NMR Restraints Analysis
  8. 3rd Party Software
    1. 3rd Party Applications
      1. Movies
      2. Codecs
  9. Python Integration
  10. Using PyMol For Unintended Uses (OpenGL Object Renderer)
    1. Arbitrary Graphics Objects

Tree 02:09, 16 Feb 2005 (CST)