PyMOL resources, books and references

NOTE: this post becoming too long, its content is now moved and updated on the page: PyMOL Resources

PyMOL resources


This post provides resources on PyMOL

What is PyMOL and how to get it

The University of Wisconsin participates in the licensing of PyMOL Campus wide. License and software are available on the Campus software library page (requires NetID.) However, the actual software can also be downloaded from the PyMOL home page.

PyMOL is a cross-platform molecular graphic software (Mac/Linux/Windows) that has been extensively used to visualize macromolecule in 3D. Numerous plugins have significantly improved PyMOL’s functionalities: macromolecular analysis, homology modeling, protein-ligand docking, pharmacophore modeling, and Molecular Dynamics (MD) simulation.

PyMOL Books

Exploring Protein Structure: Principles and Practice

Details on the book “Exploring Protein Structure: Principles and Practice” is detailed on this page “PyMOL in book Exploring Protein Structure – Principles and Practice” [Archived]

The book provides complete scripts to recreate the book figures and as such is also a valuable PyMOL resource in addition to insights in the study of protein structures.

Author: Tim Skern: Skern lab

Introduction to proteins: structure, function, and motion

Book: Introduction to Proteins Structure, Function, and Motion, Second Edition
By Amit Kessel, Nir Ben-Tal. First Published 2018. Chapman and Hall/CRC
DOI  Pages 988

Freely downloadable resources about the book: The Book Page provides downloadable materials:

•  Online Course: Recorded lectures and presentations
•  PowerPoint presentations to go with the book.
•  All figures and tables of the book
•  Membrane-Bound Proteins– chapter 7 (Sample chapter for download)
•  Animations of the book
•  PyMol Session files [Archived]
•  Exercises for each chapter (PDF)

Please acknowledge the book when using the materials.

PyMOL tutorials

The materials I developed over the years is located  onto the PyMOL page within the Molecular Graphics Tutorials page.

This includes the PDF version of the Biochemistry Graduate class as announced in the June  2019 post PyMOL Tutorial Books Released The Biochem 660 PyMOL tutorial book has been split in 4 PDFs for easier read and download:

  • Book 1: Molecular Graphics Essentials (Summary of methods to acquire 3D data; file formats)
  • Book 2: PyMOL part 1 (Graphical representations and atom selection, electrostatic potentials, side-chain mutations, 3D overlays, …)
  • Book 3: PyMOL part 2 (scripts, animations and movies, multimeric structures, morphing)
  • Book 4: PyMOL part 3 (Electron Density Maps)

Other online tutorials

Some older versions of my own tutorials are sometimes f0und on other sites

Note really a tutorial, this article in 2 parts offers a “Quick Start” method to learning PyMOL with 10 commands:

PyMOL: 10 very basic commands that you really need to know:

Translated tutorial

This PyMOL tutorial is translated from Japanese. It contains:

Specific tutorials

The Nagai Lab Guide to making the spliceosome friendly (PDF) [Archived PDF] or  “How to use PyMOL to explore the structure of the spliceosome

Aligning three-dimensional structures in PyMOL [Archived] ( This text describes how to align three dimensional molecular structures using a three dimensional molecular viewer. As an example, we align human H-RAS, N-RAS, and K-RAS structures using PyMOL. (

Analyzing a 3D Structure File [Archived] ( This text introduces how a 3D molecular viewer can be used to analyze the structure of a biological molecule. As an example, this text walks through analyzing the structure of the protein RAS using PyMOL.

PyMOL for Visualization of the BRCA2 Complex and 1N0W, 1PZN, 1MJE, 1MIU Structures [Archived]: details how the author used the visualization tool PyMOL for examining 3D representations of the aforementioned proteins, and looking into detail into various protein-protein and protein-DNA interactions.

Learn to Draw a Molecule in PyMOL in 8 Easy Steps [Archive] Uses the transcription factor AgrA from methicillin-resistant Staphylococcus aureus (MRSA) as example molecule. (Sidote DJ et al. (2008))

Online tutorial with materials

The Structural Biology Research Unit co-ordinates and promotes the experimental determination of biological structure at the University of Cape Town. The web site offers the following PyMOL materials [Archived]:

References, FAQS, and “wikis”


The main reference is the community-run PyMOL Wiki offering tutorials, scripts, detailed command references and more.


Reference Manual

A reference manual provides details on all available commands: PyMOL reference manual (PDF, 1998-2003) [Archived]

An HTML version is also available: PyMol Reference Manual containing command descriptions. (Noted as ancient and obsolete.) [Archived.]

User’s manual

PyMOL User’s Guide, written by Warren L. DeLano, Ph.D. with assistance fromb Sarina Bromberg, Ph.D. Copyright © 2004, All Rights Reserved. DeLano Scientific LLC is now Schrödinger, Inc.

In addition, an HTML version is also available User’s Reference Manual. [Archived]. Although it is labeled old and obsolete the information is useful. One of the most useful might be the Atom Selection Syntax.

Reference Cards

Reference Card (“Cheat Sheet”, from PyMOL wiki.) [Archived.]

Quick Reference Guide for Intermediate PyMOL Users (PDF, [Archived])


A short Frequently Asked Questions (FAQs) is presented by SourceForge [Archived] that still links to a long defunct web site ( page on “Bioinformatics that, fortunately, is still “alive” in the “Way Back Machine” web archive: Archived Bioinformatics page of The offered topics were/are:

Script repositories

The PyMOL Wiki contains also a Script Library.

PyMOL Wiki Scripting from page “Practical Pymol for Beginners.”

Many scripts in the Python language are available at the Queens University page “My PyMOL Script repository” [Archived]. Some of these scripts are very valuable and powerful, used for coloring, selecting or aligning structures. See page “How to execute a py script on PyMOL?” [Archived] to learn how to use the available scripts.

An additional page titled “Introduction to structural alignment with PyMOL” [Archived] is very useful to learn how to align and compare sequences.

Another source of useful scripts is available on GitHub: Pymol-script-repo

This web site “Maya Chem Tools” [Archived] contains perl and pythong scripts for multiple software. Those for PyMOL start with the root name PyMOL and end with .py.

Example: How can I evaluate the hydrophobicity of a protein with PyMol? [Archived]
Requires script “” [Archived Zip]

Useful publications

Mooers, BHM. Shortcuts for faster image creation in PyMOL. Protein Science. 2020; 29: 268276.


Sidote DJ et al. (2008) Structure of the Staphylococcus aureus AgrA LytTR domain bound to DNA reveals a beta fold with an unusual mode of binding. Structure 16:727–35