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PyMol Wiki Home

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

Moving In

Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.

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

== Initial Wiki Layout Suggestion == (Warren Delano; Tree; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)

Sections

1. Technical Issues
2. Basic Usage
3. Advanced Issues
4. Scripting
5. Plugins
6. High-level applications
7. 3rd Party Software
8. Using PyMol For Unintended Uses

Subsections

We need to put each one of these in a category above, or make a new section above where appropriate.

• Mouse Controls
• Command Language
• Atom Selections
• Ray-tracing
• Movies and Animations
• Cartoon Representations
• Settings Reference (all settings and what they do)
• Stereo 3D Display
  • Hardware Options
  • Linux XFree86 Configuration
• Crystallography Applications
  • Symmetry
  • Electron Density
• NMR Applications
  • Working with a Family of Structures
  • Superimposition and RMSD
  • NMR Restraints Analysis
• Arbitrary Graphics Objects
• Python Integration
• Scenes

• Installation
  • Hardware Requirements
  • Software Requirements
  • OS Dependent
    • Linux
    • MAC
    • Windows
    • Script Library

• Plugins/Modules
  • APBS Plugin
  • rtools Plugin

• Plugins
  • List of Plugins
  • Tutorial on writing plugins
  • Others

• Structure Alignment
  • Structure Alignment Editor
• 3rd Party Applications
  • Movies
  • Codecs

• Rendering molecules
  • Basics of displaying molecules
  • Coloring molecules
  • Displaying biochemical properties

• Modeling and editing structures.
  • Editing atoms
  • Molecular sculpting
  • Homology modeling
• How to do electrostatics and energy minimization.
• Launching PyMOL (has been asked often)
• Some kind of "script collection" would be very useful
• Creating publication-quality images HOWTO

Proposal for structure

Most of these points fall into some higher category. Here is a proposal how they could be arranged (krother):

• I. Technical issues (installation, hardware)
• II. Basic usage (controls, rendering, selections)
• III. Advanced issues (Ray tracing, settings, movies)
• IV. Scripting
• V. Plugins
• VI. High-level applications (Crystallography, NMR)

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Tree 02:09, 16 Feb 2005 (CST)

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