A self-paced tutorial for visualising protein structures using PyMOL

PyMOL is a software package used to manipulate protein structures (pdb files) determined by x-ray crystallography, NMR, cryo-EM or modelling. It is free for educational use, for open source self-builds and enables us to visualise the interactions between protein side-chains or between side-chains and ligands (including drug molecules). PyMOL is widely used and enables us to create high quality figures for publication. It also enables us to create movies for presentations.

This record contains a self-paced tutorial to enable students to master the basic features of PyMOL and create a publication-quality figure. It is suitable for computer-literate students (undergraduate and above) and for research staff. The tutorial can be completed within 2 hours and I teach it in a workshop setting with a tutor on hand to provide practical assistance. The workbook contains questions for students to complete to enable staff to gauge student understanding.

This tutorial was created using PyMOL 1.7.1.0 and is compatible with more recent versions of the software. The pdb file is a copy of PDB code 5OOP.

Version history

• v1: Original submission.
• v2: Minor updates for clarity and to correct spellings / typos etc.

Have you used this material in your teaching? If so, do get in touch and let me know how it went!