PyMOL Wiki:Community Portal: Difference between revisions

Revision as of 07:17, 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!

# 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>

See The Geshi Home Page

Tree

@@ Line 3: / Line 3: @@
 == 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 [[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 ===
@@ Line 21: / Line 15: @@
   <npython>line-numbered code here</npython>
 </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!