A self-paced tutorial for visualising protein structures using PyMOL

<p dir="ltr">Please note that following closure of NTR to new submissions at the end of June 2025, updates to this resource will be released on <a href="https://doi.org/10.5281/zenodo.15371111" rel="noreferrer" target="_blank">Zenodo</a>. The full collection of Charlotte Dodson's teaching materials has moved to <a href="https://zenodo.org/communities/charlottedodsonteaching/" rel="noreferrer" target="_blank">https://zenodo.org/communities/charlottedodsonteaching/</a>.</p><p dir="ltr">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.</p><p dir="ltr">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.</p><p dir="ltr">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.</p><h3>Version history</h3><ul><li><b>v1:</b> Original submission.</li><li><b>v2:</b> Minor updates for clarity and to correct spellings / typos etc.</li></ul><p dir="ltr">Have you used this material in your teaching? If so, do <a href="https://researchportal.bath.ac.uk/en/persons/charlotte-dodson" rel="noreferrer" target="_blank">get in touch</a> and let me know how it went!</p>