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## [[:Category:News Discussion|Discussion]]
 
## [[:Category:News Discussion|Discussion]]
 
## [[:Category:News PyMol Beta|PyMol Beta]]
 
## [[:Category:News PyMol Beta|PyMol Beta]]
 +
 
# [[:Category:Technical Issues|Technical Issues]]
 
# [[:Category:Technical Issues|Technical Issues]]
 
## [[:Category:Technical Issues Installation|Installation]]
 
## [[:Category:Technical Issues Installation|Installation]]
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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|Launching PyMOL]]
 
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
 
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
 
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
 
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
 +
 
# [[Using the GUI]]
 
# [[Using the GUI]]
 
## [[Mouse Controls]]
 
## [[Mouse Controls]]
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## [[Structure Alignment]]
 
## [[Structure Alignment]]
 
## [[Structure Alignment Editor]]
 
## [[Structure Alignment Editor]]
 +
 
# [[:Category:Commands|Command Language]]
 
# [[:Category:Commands|Command Language]]
 
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
 
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
 
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
 
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
 +
 
# [[:Category:Advanced Issues|Advanced Issues]]
 
# [[:Category:Advanced Issues|Advanced Issues]]
 
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
 
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues |Editing atoms|Editing Atoms]]
+
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
### [[:Category:Advanced Issues Molecular Sculpting|Molecular sculpting]]
+
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
### [[:Category:Advanced Issues Homology Modeling|Homology modeling]]
+
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
 
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
 
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
### [[:Category:Advanced Issues labels|labels]]
+
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
### [[:Category:Advanced Issues Photoshop and GIMP|Photoshop/GIMP]]
+
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
### [[:Category:Advanced Issues Stereo Figures|Stereo Figures]]
+
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
### [[:Category:Advanced Issues Publication Quatlity Images|Publication-quality images]]
+
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
 +
 
 
# [[:Category:Scripting|Scripting]]
 
# [[:Category:Scripting|Scripting]]
 
## [[:Category:Scripting Example Scripts|Example Scripts]]
 
## [[:Category:Scripting Example Scripts|Example Scripts]]
Line 87: Line 93:
 
# [[:Category:Plugins|Plugins]]
 
# [[:Category:Plugins|Plugins]]
 
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
 
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[:Category:Plugins APBS| APBS Plugin]]
+
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
 
## [[:Category:Plugins rtools | rtools]]
 
## [[:Category:Plugins rtools | rtools]]
 
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
 
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
 
## [[:Category:Plugins Others| Others]]
 
## [[:Category:Plugins Others| Others]]
 +
 
# [[:Category:High-Level Applications|High-Level Applications]] (Crystallography, NMR)
 
# [[:Category:High-Level Applications|High-Level Applications]] (Crystallography, NMR)
 
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
 
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
Line 96: Line 103:
 
### [[:Category:High-Level Applications Electron Density|Electron Density]]
 
### [[:Category:High-Level Applications Electron Density|Electron Density]]
 
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
 
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[:Category:High-Level Applications Working with a Family of Structures|Working with Structure Families]]
+
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
### [[:Category:High-Level Applications Superimposition and RMSD|Superimposition and RMSD]]
+
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[:Category:High-Level Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
+
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
 +
 
 
# [[:Category:Third Party Software|Third Party Software]]
 
# [[:Category:Third Party Software|Third Party Software]]
 
## [[:Category:Third Party Software Movies|Movies]]
 
## [[:Category:Third Party Software Movies|Movies]]
 
## [[:Category:Third Party Software Codecs|Codecs]]
 
## [[:Category:Third Party Software Codecs|Codecs]]
 +
 
# [[:Category:Python Integration|Python Integration]]
 
# [[:Category:Python Integration|Python Integration]]
 +
 
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
 
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
 
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
 
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
 +
 
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
 
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
 +
 
----
 
----
 
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
 
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
 
----
 
----

Revision as of 03:11, 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
  1. Technical Issues
    1. Installation
      1. OS Dependent
        1. Linux
        2. MAC
        3. Windows
  1. Launching PyMOL
    1. Command Line Options
    2. Launching From a Script
  1. 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
  1. Command Language
    1. PyMOL Command Script
    2. PyMOL Python API
  1. Advanced Issues
    1. Modeling and editing structures
      1. Editing Atoms
      2. Molecular sculpting
      3. Homology modeling
    2. Image Manipulation
      1. labels
      2. Photoshop/GIMP
      3. Stereo Figures
      4. Publication-quality images
  1. Scripting
    1. Example Scripts
    2. Script Library
  2. Plugins
    1. How to do electrostatics and energy minimization.
      1. APBS Plugin
    2. rtools
    3. Tutorial on writing plugins
    4. Others
  1. 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
  1. Third Party Software
    1. Movies
    2. Codecs
  1. Python Integration
  1. Unintended Uses (OpenGL Object Renderer)
    1. Arbitrary Graphics Objects
  1. Uncategorized For new pages, misplaced pages, etc.

Tree 02:09, 16 Feb 2005 (CST)