PyMOLWiki:Community Portal

How to Get Involved

• First, go sign up, if you don't already have an account. New accounts can be created from any page; see the upper right hand side of any given page.

What to Do

• If you have a powerful little script you wrote and enjoy using, upload it and let the world know about it.
• Each of the commands, needs many many nice examples of usage. Feel free to expound (and comment on) the commands.
• More internal linking (from page to page) is needed.
• We also need a way to make things easier to find on the wiki.

Features

New! GeShi: Syntax Highlighting for Python & More

Use Geshi for syntax highlighting your Python code! 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)!

<npython>

1. 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

Paid Documentation?

I might be interested in using PyMOL, but I don't like the fact that I have to pay for documentation. I don't even know what I'm missing out on, and I don't know if it's worth trying out PyMOL, or becoming actively involved in its development (or simply the creation of content on this wiki). Guaka 07:28, 5 September 2007 (CDT)

Huh? You don't have to pay for documentation. PyMOLWiki is freely accessible, and it contains far more useful content than the "official" docs. You can also easily try out PyMOL without compiling the current open-source code by downloading older free builds or the current evaluation build. Nobody has to pay for PyMOL -- it's open source! Warren 20:51, 12 November 2007 (CST)