Git script guidelines
Guide lines
To make a good PyMOL wiki page, you can follow some few guidelines. Some should be seen as mandatory, and are marked.
Categories
You also should put you script in a category. See categories here: http://www.pymolwiki.org/index.php/Category:Script_Library
You add your script to a category, by writing these lines in the end of the wiki page. Examples:
[[Category:Script_Library]] [[Category:Structural_Biology_Scripts]]
Template for a new page
The following sections, can for example be copied to a new page.
You can find tips for formatting a mediawiki page here: http://www.mediawiki.org/wiki/Help:Formatting
Author
This pymol script is made by you
Introduction
A little section about what the script can do, and maybe why it has been developed and under which protein discipline it is particularly useful.
Functions
If there are more than one function, you could list them here.
- Make a dot
- Write under same dot
Example of use
Here you write some example of use. Try to make examples, that anyone can access right away.
Do this by fetching proteins, and if you need other example files, but them in: Pymol-script-repo/files_for_examples
<syntaxhighlight lang="python">
import colorbydisplacement
fetch 1HP1, async=0
fetch 1HPU, async=0
hide everything
### Select asymmetric units from pdb file
create O5NT, /1HP1//A
create C5NT, /1HPU//C
delete 1HP1
delete 1HPU
show cartoon, O5NT
show cartoon, C5NT
ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
Python Code
This code has been put under version control. In the project, Pymol-script-repo.
For a color coded view:
https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/colorbydisplacement.py
See the raw code or download manually, by right clicking the following link here -> Save as: colorbydisplacement.py
https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py
References
If you have used a particular article or figure to get inspiration to your script, then make a reference.