PyMOLWiki:Community Portal
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.
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
- 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') </npython>