PyMOLWiki:Community Portal

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Revision as of 13:55, 28 February 2005 by Tree (talk | contribs) (New! GeShi: Syntax Highlighting for Python & More)
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CP

Look here for ways to get involved in the PyMolWiki!

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.

Categories/Content

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

Section Layout

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. Ray-tracing
    9. Settings Reference
    10. Movies and Animations
    11. Structure Alignment
    12. 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. PovRay
    2. Movies
    3. 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)


New! GeShi: Syntax Highlighting for Python & More

Update: I have added the option for numbered syntax highlighting and non-numbered.

 <source lang="python">Non line-numbered code here</source>
 <npython>line-numbered code here</npython>


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')

Now with line numbers!

<npython>

# axes.py

from pymol.cgo import * from pymol import cmd from pymol.vfont import plain

  1. create the axes object, draw axes with cylinders coloured red, green,
  2. 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,
  ]
  1. add labels to axes object (requires pymol version 0.8 or greater, I
  2. 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]])

  1. then we load it into PyMOL

cmd.load_cgo(obj,'axes') </npython>


See The Geshi Home Page

Tree