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PyMol Wiki Home

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

Helping

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

• 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
• Smoothing out the edges: Editors are needed just to fix our typos!
• 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!

Tree

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.

Layout Schema

1. Technical Issues (installation, hardware)
   1. Installation
      1. OS Dependent
         1. Linux
         2. MAC
         3. Windows
2. Graphics
   1. Stereo 3D Display
      1. Hardware Options
      2. Linux XFree86 Configuration
3. Basic Usage (controls, rendering, selections)
   1. Launching PyMOL (has been asked often)
   2. Interface
      1. Mouse Controls
   3. Atom Selections
   4. Concepts/Basics of displaying molecules
      1. Cartoon Representations
      2. Rendering molecules
         1. Coloring molecules
         2. Displaying biochemical properties
   5. Command Language
   6. Ray-tracing
   7. Movies and Animations
      1. Scenes
   8. Settings Reference (all settings and what they do)
   9. Structure Alignment
      1. Structure Alignment Editor
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. Script Library
   2. Some kind of "script collection" would be very useful
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

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Tree 02:09, 16 Feb 2005 (CST)

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