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 obtain 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)


For many years I participated in the teaching of Prof. Ann Palmenberg classes, in particular teaching about molecular graphics on the Desktop at a time when computer use in the classroom was not yet preeminent. This class was a useful complement to the main topic of Sequence Analysis and (molecular) Evolution also using computers.

I personally used what was called “Unix Workstations” (Silicon Graphics, sgi) which had powerful graphics and rather beautiful “photorealistic” renderings. For teaching molecular graphics on the Desktop, I first used Rasmol (see tutorial link below,) which was an amazing software fitting in about half of a 3.5” floppy disk or about 500 kilobytes. Rasmol included a sophisticated line command language but lacked the beautiful “photorealistic” renderings of the workstations. This was remedied by adding two other software in the course, one for the “publication quality renderings” (VMD) and the other for the modeling abilities of side-chain mutations and automated 3D superimposition of structures (Swiss PDB viewer later called DeepView.)

When PyMOL was still in preliminary development at version 0.99 I spent one intense week porting all the class material to PyMOL. Now, rather than using three different software, all was possible with only PyMOL. Over the years I extended and updated the PyMOL course material.

The UW-Madison Biochemistry students were the primary audience for these classes in courses Biochem 660 and 712, and occasionally in Biochem 511. I offered the PyMOL class in Biochem 660 for over a decade. The PyMOL tutorial and preliminary molecular graphics and file format introduction were part of a very large, made-to-order physical copy of a class book of about 500 pages that also contained tutorials on using other software. The PyMOL section was about 200 pages.

2017 was the last year that Biochem 660 was offered. I have therefore decided to release the complete PyMOL tutorial which you will find split in multiple PDF files. In this final revision, I had updated all web pages, and added links to archived pages when web site were defunct to keep the text as relevant as possible for future use.

(Note that this is the latest version that would supersede  any PDF “floating” on the Internet from perhaps 2006 or 2008.)

I hope that it will be useful to you in accomplishing your molecular graphics goals.


Jean-Yves Sgro, Ph.D.
Distinguished Scientist | Senior Scientist
Biotechnology Center      | Biochemistry Department
University of Wisconsin-Madison – USA
Formerly at the Institute for Molecular Virology and VirusWorld web sitecreator.

P.S. My last Rasmol tutorials are available as archives from July 18, 2002