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#### [[MAC]]
 
#### [[MAC]]
 
#### [[Windows]]
 
#### [[Windows]]
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# [[Graphics]]
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# [[Using the GUI]]
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## [[Launching PyMOL (has been asked often)]]
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## [[Mouse Controls]]
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## [[Objects and Selections]]
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### [[Working with Objects]]
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### [[Working with Selections]]
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### [[Representations]]
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#### [[Lines]]
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#### [[Sticks]]
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#### [[Cartoon]]
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#### [[Surface]]
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#### [[Mesh]]
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#### [[Spheres]]
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#### [[Dots]]
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### [[Color]]
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### [[Displaying biochemical properties]]
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## [[Display Settings]]
 
## [[Stereo 3D Display]]
 
## [[Stereo 3D Display]]
 
### [[Hardware Options]]
 
### [[Hardware Options]]
 
### [[Linux XFree86 Configuration]]
 
### [[Linux XFree86 Configuration]]
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# [[Basic Usage (controls, rendering, selections)]]
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## [[Scenes]]
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## [[Launching PyMOL (has been asked often)]]
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## [[Mouse Settings]]
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## [[Interface]]
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## [[Wizards]]
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### [[Mouse Controls]]
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## [[Plugins]]
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## [[Atom Selections]]
 
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## [[Concepts/Basics of displaying molecules]]
 
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### [[Cartoon Representations]]
 
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### [[Rendering molecules]]
 
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#### [[Coloring molecules]]
 
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#### [[Displaying biochemical properties]]
 
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## [[:Category:Commands|Command Language]]
 
 
## [[Ray-tracing]]
 
## [[Ray-tracing]]
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## [[Settings Reference (all settings and what they do)]]
 
## [[Movies and Animations]]
 
## [[Movies and Animations]]
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### [[Scenes]]
 
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## [[Settings Reference (all settings and what they do)]]
 
 
## [[Structure Alignment]]
 
## [[Structure Alignment]]
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### [[Structure Alignment Editor]]
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## [[Structure Alignment Editor]]
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# [[:Category:Commands|Command Language]]
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## [[PyMOL Command Script]]
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## [[PyMOL Python API]]
 
# [[Advanced Issues]] (Ray tracing, settings)
 
# [[Advanced Issues]] (Ray tracing, settings)
 
## [[Launching PyMOL (has been asked often)]]
 
## [[Launching PyMOL (has been asked often)]]
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# [[Scripting]]
 
# [[Scripting]]
 
## [[Script Library]]
 
## [[Script Library]]
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## [[Some kind of "script collection" would be very useful]]
 
 
# [[Plugins]]
 
# [[Plugins]]
 
## [[List of Plugins]]
 
## [[List of Plugins]]

Revision as of 18:07, 17 February 2005

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

  • 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!

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. Using the GUI
    1. Launching PyMOL (has been asked often)
    2. Mouse Controls
    3. Objects and Selections
      1. Working with Objects
      2. Working with Selections
      3. Representations
        1. Lines
        2. Sticks
        3. Cartoon
        4. Surface
        5. Mesh
        6. Spheres
        7. Dots
      4. Color
      5. 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
    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. 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)

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