This practical course aim to introduce molecular visualization software to 3rd year student through the Pymol Software. This course is under the direction of Gautier Moroy in University Paris 7 – Diderot. You will find of this page TD files and some advises that I can give a lot during theses lessons.
Installation on your own computer
If you want to install PyMOL on your personal computer, go to this page, I explain how to install the last version on Windows and Linux.
Useful link :
- PyMOL Wiki : http://www.pymolwiki.org/. On this wiki you will find a lot of trick, help for some commands, how to obtained certain visualization.
- PyMOL Cheat sheet (from PyMOL wiki) : PymolRef.pdf
- PyMOL Scripts repo : http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/. On this page you will find some scripts which you can execute on PyMOL. If you need some help to run it, go to this page .
- another PyMOL Scripts repo : https://github.com/Pymol-Scripts/Pymol-script-repo
FAQ (Frequently Asked Question)
How can I color amino acids by they name or a color code?
Unfortunatly Pymol does not have a built-in function to do that….
Fortunaly we can create our own functions =D
I’ve made a script to color amino acids by a color-blind adapted color code .
- Download the script below
- Refer to this page on the Tutorial section if you don’t know how to execute it.
I Can’t manage to load a PDB (ascii error or Unicode Error).
Pymol doesn’t allow a non-classic character on the file path (accent, space etc…). Change the location of your pdb file or script file.
 Taylor, W. R. (1997). Residual colours: a proposal for aminochromography. Protein Engineering, 10(7), 743–6.