NOTE: this post becoming too long, its content is now moved and updated on the page: PyMOL Resources
PyMOL resources
Summary
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 https://doi.org/10.1201/9781315113876 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
- Older but noteworthy is the 2009 “Introduction to PyMOL” (PDF) by Delano [Archived PDF].
- A Simple Tutorial for PyMOL (14 pages, cerca 2019, by Dr Dafydd Jones School of Biosciences, Cardiff University) [Archived PDF]
- PyMOL hand out [Archived] from Partnership for Structural Biology, Grenoble, France
- Chem 110L: Macromolecular Visualization Laboratory Exercise: PyMOL (2004- 2009 -by Dr. Kalju Kahn, Department of Chemistry and Biochemistry, UC Santa Barbara.) [Archived – HTML]
- A Beginner’s Guide to Molecular Visualization Using PyMOL (August 2012, 14 pages, by Nicholas Fitzkee, Mississippi State University.)
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:
- PyMOL: 10 very basic commands that you really need to know- Part 1 [Archived]
- PyMOL: 10 very basic commands that you really need to know- Part 2 [Archived but “blinks”]
Translated tutorial
This PyMOL tutorial is translated from Japanese. It contains:
- Hydrogen bond
- PyMOL Interaction interface
- PyMOL Conservation
- PyMOL Electrostatic potential
- PyMOL Hydrophobicity
- PyMOL Installation
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] (labxchange.org): 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. (labxchange.org)
Analyzing a 3D Structure File [Archived] (labxchange.org):
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]:
- Pymol tutorial: pymol_tut (Zip.) [Archived Zip]
- Pymol User Manual: pymol-user-manual.pdf
- Pymol Reference Manual: pymol-reference-manual.pdf (not found on this web site. See below.)
References, FAQS, and “wikis”
Wiki
The main reference is the community-run PyMOL Wiki offering tutorials, scripts, detailed command references and more.
References
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])
FAQs
A short Frequently Asked Questions (FAQs) is presented by SourceForge [Archived] that still links to a long defunct web site (www.rubor.de) page on “Bioinformatics that, fortunately, is still “alive” in the “Way Back Machine” web archive: Archived Bioinformatics page of www.rubor.de. The offered topics were/are:
- Launching PyMOL
- Displaying biochemical properties
- Coloring molecules
- Rendering molecules
- Modeling with PyMOL
- Movies
- Advanced PyMOL features
- Python scripting
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 “color_h.py” [Archived Zip]
Useful publications
References
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