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PyMol Wiki Home

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

Go!

You may now add content to the wiki. This is a semi-structured wiki in that the categories are pseudo-hierarchically linked.

New Categories/Content

If you feel we're missing a category, please find where it would most logically fit, add it to the main page via the Top Level Schema Policy.

Helping

• A wiki edit/user policy is needed.
• 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
• 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!

GeShi: Syntax Highlighting for Python & More

We now have a syntax highlighter installed. It now supports something like 28 programming languages! When you paste your code simply wrap it in <language_name> ... code here ... </language_name>.

Here's an example:

<python>
  # axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
   CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
   CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
   CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
   ]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')

<python>

gives us the code

 # axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
   CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
   CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
   CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
   ]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')

See The Geshi Home Page

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 PyMol
   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 -- wrong place
      1. Hardware Options -- wrong place?
      2. Linux XFree86 Configuration -- wrong place
   5. Scenes
   6. Mouse Settings
   7. Wizards
   8. Plugins -- wrong place?
   9. Ray-tracing
   10. [[:Category:Using Pymol Settings Reference|Settings Reference
   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
      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
   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.

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Tree 02:09, 16 Feb 2005 (CST)

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