Postgraduate bioinformatics and molecular modelling course – 2024
Basic Biomedical Sciences Postgraduate Program
Universidad Autónoma de San Luis Potosí, Faculty of Medicine.
From March 4th to May 9th, 2024.
Semester: 2nd semester
Type: On-site theoretical classes and workshop.
Total allocated time: 60 hours
Number of credits: 7.5
Schedule: Monday through Friday from 16:30 to 18:00
Students must supply their wifi-capable personal laptop computers including
three-button mouse with scroll-wheel, wall adaptor and note-pad to each session.
Students will require administrative rights to their laptop to allow installation
of PyMol Desktop Version 2.5.8 (Updated January 18th 2024) by
Schrödinger
Operating system and hardware requirements:
64-bit Windows 10 or newer
64-bit macOS 10.12+, including Apple Silicon (M1) with Rosetta 2
64-bit Linux, including CentOS 7+, Ubuntu 18.04+, and others (glibc 2.12+)
Must-read bibliography
1. Boosting the Full Potential of PyMOL with Structural Biology Plugins.
Rosignoli S, Biomolecules. 2022 Nov 27;12(12):1764. (Open Access)
2. Molecular Graphics: Bridging Structural Biologists and Computer Scientists.
Martinez X, Structure. 2019 Nov 5;27(11):1617-1623. (Open Access)
3. Templates for writing PyMOL scripts.
Mooers BHM, Protein Sci. 2021 Jan;30(1):262-269. (Open Access)
4. A PyMOL snippet library for Jupyter to boost researcher productivity.
Mooers BHM, Comput Sci Eng. 2021 Mar-Apr;23(2):47-53. (Open Access)
5. Shortcuts for faster image creation in PyMOL.
Mooers BHM, Protein Sci. 2020 Jan;29(1):268-276. (Open Access)
6. Using the PyMOL application to reinforce visual understanding of protein structure.
Rigsby RE, Biochem Mol Biol Educ. 2016 Sep 10;44(5):433-7. (Open Access)
7. Using a PyMOL activity to reinforce the connection between genotype and phenotype in an undergraduate genetics laboratory.
Simmons AD, PLoS One. 2014 Dec 2;9(12):e114257. (Open Access)
PyMol Homework based on previous publication
Additional PyMol Homework based on previous publication
Supporting videos
1. Understanding Crystallography - Part 1: From Proteins to Crystals.
The Royal Institution video
2. Understanding Crystallography - Part 2: From Crystals to Diamond.
The Royal Institution video
3. Protein crystallography.
spring8channel video
4. X-Ray Diffraction (XRD) Basic Operation.
Zachary Neale video)
5. Fundamentals of NMR Spectroscopy.
The United ChemDom video
6. Protein Data Bank at 50 years of age | Stephen Burley.
RCSBProteinDataBank video
7. Cryo-FIB milling and membrane-bound proteins.
Mike Martynowycz HHMI/UCLA at
RCSBProteinDataBank
8. Pymol for beginners | Basic Tutorial Molecular Visualization of Proteins | Bioinformatics.
Bioinformatics With BB video
9. Molecular Visualization Using PyMOL: 1 Introduction/User Interface.
Brown Lab video
10. PyMOL tutorial 1: Introduction and using the GUI.
PyMOL Ross video
11. PyMOL tutorial 2 : Making selections and using commands.
PyMOL Ross video
12. PyMOL tutorial 3 : Publication Quality Images.
PyMOL Ross video
13. PyMOL tutorial 4 : Making Movies.
PyMOL Ross video
14. PyMOL tutorial 5 : Building and Manipulating.
PyMOL Ross video
15. PyMOL tutorial 6 : FAQ - proximity selection, recording data, electron density.
PyMOL Ross video
16. PyMOL Quickie - Making Mutations.
PyMOL Ross video
17. PyMOL: Active Sites.
Molecular Memory video
18. Pymol Advanced Session, Protein Ligand Interactions.
Bioinformatics With BB video
Reference texts and pages
PyMol Wiki (What-I-Know-Is.
Hosted by SB Grid Consortium.
Steve's PyMol Cheat Sheet.
Peak Proteins Protocols.
PyMolWiki Cheat Sheet
Hosted by SB Grid Consortium.
Quick Reference Guide for Intermediate PyMOL Users
DeLano Scientific LLC.
