PyMOLWiki:Community Portal: Difference between revisions

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== Helping ==
== 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
* 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 [[User:Tree|Tree]].
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|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 ===
=== New! GeShi: Syntax Highlighting for Python & More ===
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  <npython>line-numbered code here</npython>
  <npython>line-numbered code here</npython>
</pre>
</pre>
We now have a syntax highlighter installed.  It now supports something like 28 programming languages!  When you paste your code simply wrap it in
&lt;language_name&gt; ... code here ... &lt;/language_name&gt;. 
Here's an example:
<pre>
&lt;python&gt;
  # 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')
&lt;python&gt;
</pre>
gives us the code
<source lang="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')
</source>


Now with line numbers!
Now with line numbers!

Revision as of 02:17, 2 March 2005

CP

Look here for ways to get involved in the PyMolWiki!

Helping

  • 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!

<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

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