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.

Tips and tricks

Use of module syntaxhighlight

You can see here, that PyMOL wiki has the SyntaxHighlight module installed.
Supported languages for Highlighting is listed here.

 <syntaxhighlight lang="python">
 </syntaxhighlight>

Use of module include

If your code section is very small, and you want to show it directly at the PyMOL wiki page, you can fetch the code directly from Github and show it on the Wiki page. Read more here.

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.