Git script guidelines

Guide lines

To make a good PyMOL wiki page, consider these guidelines.

1. Make sure that filename for script and wiki page is small and the same.

   You can redirect and copy history for a wikipage, by using the move button. It is located "top right" under the arrow, next to the search box.

   Or you can make a redirect, from another page. Write only this in the wiki page: #REDIRECT [[scriptname]]

2. Function name should in generally not contain big letters. Instead use "underscore".

   ColorByDisplacementAll should instead be named: colorbydisplacement_all

3. Make sure that there are examples how to import and use script.
4. The code reference part should be almost exactly as in the example here in this post.
5. Strongly consider to add figures to your post.
6. Make a description in the top of script by using three primes ''' Text '''.

   This text will be displayed in PyMOL, when one writes: help(scriptname)

'''
Described at PyMOL wiki:
http://www.pymolwiki.org/index.php/scriptname

Authors : yourname
Date    : July 2012
'''

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.

Put your example code snip, within these brackets.

 <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 available 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 can write a link to the protein in the example
http://www.proteopedia.org/wiki/index.php/3ig7

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

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

Download: colorbydisplacement.py

This code has been put under version control in the project Pymol-script-repo

References

If you have used a particular article or figure to get inspiration to your script, then make a reference.

Title of reference. Author name. Journal name. Vol 08/12/2012, p. 54, fig. 5 doi:10.1016/0301-0104(89)87019-3