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Revision as of 14:05, 23 March 2005 by Krother (talk | contribs)
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Look here for ways to get involved in the PyMolWiki!

Editors, you can upload images for your examples and supporting text! Check out Special:Upload.

Working with Categories

To assign pages to categories, use tags at the end of your page containing the category, sub-category and the page name.

Example: There is a page 'Publication Quality Images' in the category 'Advanced Issues' and the sub-category 'Image Manipulation'. It has the tag:

[[Category:Advanced_Issues_Image_Manipulation|Publication Quality Images]]


  • 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.

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>

Now with line numbers (or not)!



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