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#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
 
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
 
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
 
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
 +
# [[:Category:Launching PyMOL|Launching PyMOL]]
 +
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
 +
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
 
# [[Using the GUI]]
 
# [[Using the GUI]]
## [[Launching PyMOL]]
 
### [[Command Line Options]]
 
### [[Launching From a Script]]
 
 
## [[Mouse Controls]]
 
## [[Mouse Controls]]
 
## [[Objects and Selections]]
 
## [[Objects and Selections]]
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## [[Structure Alignment Editor]]
 
## [[Structure Alignment Editor]]
 
# [[:Category:Commands|Command Language]]
 
# [[:Category:Commands|Command Language]]
## [[PyMOL Command Script]]
+
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
## [[PyMOL Python API]]
+
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
# [[Advanced Issues]] (Ray tracing, settings)
+
# [[:Category:Advanced Issues|Advanced Issues]]
## [[Launching PyMOL (has been asked often)]]
+
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
## [[Advanced Atom Selections]]
+
### [[:Category:Advanced Issues |Editing atoms|Editing Atoms]]
## [[Modeling and editing structures.]]
+
### [[:Category:Advanced Issues Molecular Sculpting|Molecular sculpting]]
### [[Editing atoms]]
+
### [[:Category:Advanced Issues Homology Modeling|Homology modeling]]
### [[Molecular sculpting]]
+
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
### [[Homology modeling]]
+
### [[:Category:Advanced Issues labels|labels]]
## [[Image Manipulation]]
+
### [[:Category:Advanced Issues Photoshop and GIMP|Photoshop/GIMP]]
### [[labels]]
+
### [[:Category:Advanced Issues Stereo Figures|Stereo Figures]]
### [[Photoshop/GIMP]]
+
### [[:Category:Advanced Issues Publication Quatlity Images|Publication-quality images]]
### [[Stereo Figures]]
+
# [[:Category:Scripting|Scripting]]
### [[Creating publication-quality images HOWTO]]
+
## [[:Category:Scripting Example Scripts|Example Scripts]]
# [[Scripting]]
+
## [[:Category:Scripting Script Library|Script Library]]
## [[Example Scripts]]
 
## [[Script Library]]
 
 
# [[:Category:Plugins|Plugins]]
 
# [[:Category:Plugins|Plugins]]
## [[How to do electrostatics and energy minimization.]]
+
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[APBS Plugin]]
+
### [[:Category:Plugins APBS| APBS Plugin]]
## [[rtools Plugin]]
+
## [[:Category:Plugins rtools | rtools]]
## [[Tutorial on writing plugins]]
+
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [[Others]]
+
## [[:Category:Plugins Others| Others]]
# [[High-level applications]] (Crystallography, NMR)
+
# [[:Category:High-Level Applications|High-Level Applications]] (Crystallography, NMR)
## [[Crystallography Applications]]
+
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
### [[Symmetry]]
+
### [[:Category:High-Level Applications Symmetry|Symmetry]]
### [[Electron Density]]
+
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[NMR Applications]]
+
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[Working with a Family of Structures]]
+
### [[:Category:High-Level Applications Working with a Family of Structures|Working with Structure Families]]
### [[Superimposition and RMSD]]
+
### [[:Category:High-Level Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[NMR Restraints Analysis]]
+
### [[:Category:High-Level Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
# [[3rd Party Software]]
+
# [[:Category:Third Party Software|Third Party Software]]
## [[3rd Party Applications]]
+
## [[:Category:Third Party Software Movies|Movies]]
### [[Movies]]
+
## [[:Category:Third Party Software Codecs|Codecs]]
### [[Codecs]]
+
# [[:Category:Python Integration|Python Integration]]
# [[Python Integration]]
+
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
+
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
## [[Arbitrary Graphics Objects]]
 
 
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
 
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
 
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[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
 
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
 
----
 
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Revision as of 03:07, 18 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.

Please see Discussion for more thoughts on the site organizaiton.

Layout Schema

  1. News
    1. Discussion
    2. PyMol Beta
  2. Technical Issues
    1. Installation
      1. OS Dependent
        1. Linux
        2. MAC
        3. Windows
  3. Launching PyMOL
    1. Command Line Options
    2. Launching From a Script
  4. Using the GUI
    1. Mouse Controls
    2. 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
    3. Display Settings
    4. Stereo 3D Display
      1. Hardware Options
      2. Linux XFree86 Configuration
    5. Scenes
    6. Mouse Settings
    7. Wizards
    8. Plugins
    9. Ray-tracing
    10. Settings Reference (all settings and what they do)
    11. Movies and Animations
    12. Structure Alignment
    13. Structure Alignment Editor
  5. Command Language
    1. PyMOL Command Script
    2. PyMOL Python API
  6. Advanced Issues
    1. Modeling and editing structures
      1. Editing atoms|Editing Atoms
      2. Molecular sculpting
      3. Homology modeling
    2. Image Manipulation
      1. labels
      2. Photoshop/GIMP
      3. Stereo Figures
      4. Publication-quality images
  7. Scripting
    1. Example Scripts
    2. Script Library
  8. Plugins
    1. How to do electrostatics and energy minimization.
      1. APBS Plugin
    2. rtools
    3. Tutorial on writing plugins
    4. Others
  9. High-Level Applications (Crystallography, NMR)
    1. Crystallography Applications
      1. Symmetry
      2. Electron Density
    2. NMR Applications
      1. Working with Structure Families
      2. Superimposition and RMSD
      3. NMR Restraints and Analysis
  10. Third Party Software
    1. Movies
    2. Codecs
  11. Python Integration
  12. Unintended Uses (OpenGL Object Renderer)
    1. Arbitrary Graphics Objects
  13. Uncategorized For new pages, misplaced pages, etc.

Tree 02:09, 16 Feb 2005 (CST)