Main Page

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; Roger Dodd)

Sections

1. Technical Issues (installation, hardware)
2. Basic Usage (controls, rendering, selections)
3. Advanced Issues (Ray tracing, settings)
4. Scripting
5. Plugins
6. 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
7. 3rd Party Software
8. Using PyMol For Unintended Uses (OpenGL Object Renderer)

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)
• Graphics
  • Stereo 3D Display
    • Hardware Options
    • Linux XFree86 Configuration
• 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
  • Image Manipulation
    • labels
    • Photoshop/GIMP
    • Stereo Figures

• 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

link title

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)

---

Tree 02:09, 16 Feb 2005 (CST)

---