PyMOL in book Exploring Protein Structure – Principles and Practice
This textbook introduces the basics of protein structure and logically explains how to use online software to explore the information in protein structure databases.
This textbook introduces the basics of protein structure and logically explains how to use online software to explore the information in protein structure databases.
PyMOL is a great program that runs natively on all 3 major platforms. However, I wanted to use a docker image that allegedly can run PyMOL (albeit an older version 1.8.2.) The reason might not be apparent at first but while the 3D interactivity would be slow, there can be other reason such a contraption …
In 1992 I attended a molecular graphics visualization and simulation somewhere in Texas, organized by Keck. One of the presenter had a movie of molecular dynamics of a protein that forever changed my mental view of the 3D structure of a protein: the atoms “wiggled” and it made clear with a stunning visual depiction that …
A couple years ago I wrote a short note on another blog (DNA.today – link below) about a web site that can be quite useful: it provides the name of alternate software. The site is: alternativeto.net For example, if you cannot afford Adobe PhotoShop you would be glad to find an alternative in “Gimp” (GNU Image Manipulation Program.) The …
Edit: April 8, 2025 Images were updated to remove the error that presented the roadmap in a mirror image. Docker saves the day! Here is a great example of how Docker can help save a NATURE paper! Summary: Problem: Professor wants to use a specific virology program called rivem (links below.) However, this only works on …
A small chapter At the turn of the Century (from XX to XXI) I was invited to write a small chapter on the visualization of virus structure for a book that would be published in Spanish called “Principios de Virología” by Professor Jorge Ossa Londoño (CV) from the Universidad de Antioquia. (His UW Alumni Profile “Jorge Ossa …
Summary: The Biochem 660 PyMOL tutorial book has been split in 4 PDFs for easier read and download: Preamble 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 …