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You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.
 
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.
  
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== Moving In ==
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=== Helping ===
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Please excuse the mess as we create the PyMolWiki site.  The wiki will be a valuable educational & reference tool for PyMol users.
 
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== 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
 
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
  
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[[User:Tree|Tree]]
 
[[User:Tree|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.
  
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== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols; Roger Dodd)
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=== Layout Schema ===
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# [[Technical Issues]] (installation, hardware)
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== Sections ==
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## [[Installation]]
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# Technical Issues (installation, hardware)
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### [[OS Dependent]]
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# Basic Usage (controls, rendering, selections)
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#### [[Linux]]
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# Advanced Issues (Ray tracing, settings)
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#### [[MAC]]
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# Scripting
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#### [[Windows]]
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# Plugins
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# [[Graphics]]
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# High-level applications (Crystallography, NMR)
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## [[Stereo 3D Display]]
 +
### [[Hardware Options]]
 +
### [[Linux XFree86 Configuration]]
 +
# [[Basic Usage (controls, rendering, selections)]]
 +
## [[Launching PyMOL (has been asked often)]]
 +
## [[Interface]]
 +
### [[Mouse Controls]]
 +
## [[Atom Selections]]
 +
## [[Concepts/Basics of displaying molecules]]
 +
### [[Cartoon Representations]]
 +
### [[Rendering molecules]]
 +
#### [[Coloring molecules]]
 +
#### [[Displaying biochemical properties]]
 +
## [[Command Language]]
 +
## [[Ray-tracing]]
 +
## [[Movies and Animations]]
 +
### [[Scenes]]
 +
## [[Settings Reference (all settings and what they do)]]
 +
## [[Structure Alignment]]
 +
### [[Structure Alignment Editor]]
 +
# [[Advanced Issues]] (Ray tracing, settings)
 +
## [[Launching PyMOL (has been asked often)]]
 +
## [[Advanced Atom Selections]]
 +
## [[Modeling and editing structures.]]
 +
### [[Editing atoms]]
 +
### [[Molecular sculpting]]
 +
### [[Homology modeling]]
 +
## [[Image Manipulation]]
 +
### [[labels]]
 +
### [[Photoshop/GIMP]]
 +
### [[Stereo Figures]]
 +
### [[Creating publication-quality images HOWTO]]
 +
# [[Scripting]]
 +
## [[Script Library]]
 +
## [[Some kind of "script collection" would be very useful]]
 +
# [[Plugins]]
 +
## [[List of Plugins]]
 +
## [[How to do electrostatics and energy minimization.]]
 +
### [[APBS Plugin]]
 +
## [[rtools Plugin]]
 +
## [[Tutorial on writing plugins]]
 +
## [[Others]]
 +
# [[High-level applications]] (Crystallography, NMR)
 
## [[Crystallography Applications]]
 
## [[Crystallography Applications]]
 
### [[Symmetry]]
 
### [[Symmetry]]
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### [[Superimposition and RMSD]]
 
### [[Superimposition and RMSD]]
 
### [[NMR Restraints Analysis]]
 
### [[NMR Restraints Analysis]]
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# 3rd Party Software
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# [[3rd Party Software]]
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# Using PyMol For Unintended Uses (OpenGL Object Renderer)
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## [[3rd Party Applications]]
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### [[Movies]]
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=== Subsections ===
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### [[Codecs]]
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We need to put each one of these in a category above, or make a new section above where appropriate.
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# [[Python Integration]]
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<br>
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# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
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+
## [[Arbitrary Graphics Objects]]----
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* [[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]]
 
−
[http://www.example.com link title]
 
−
 
 
−
== [[Proposal for structure]] ==
 
−
Most of these points fall into some higher category. Here is a proposal how they could be arranged ([[User:Kristian Rother|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)
 
−
 
 
−
----
 
 
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
 
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
 
----
 
----

Revision as of 16:23, 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

  • 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

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. Graphics
    1. Stereo 3D Display
      1. Hardware Options
      2. Linux XFree86 Configuration
  3. Basic Usage (controls, rendering, selections)
    1. Launching PyMOL (has been asked often)
    2. Interface
      1. Mouse Controls
    3. Atom Selections
    4. Concepts/Basics of displaying molecules
      1. Cartoon Representations
      2. Rendering molecules
        1. Coloring molecules
        2. Displaying biochemical properties
    5. Command Language
    6. Ray-tracing
    7. Movies and Animations
      1. Scenes
    8. Settings Reference (all settings and what they do)
    9. Structure Alignment
      1. Structure Alignment Editor
  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
    2. Some kind of "script collection" would be very useful
  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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