This textbook introduces the basics of protein structure and logically explains how to use online software to explore the information in protein structure databases.
Molecular Graphics
Docker PyMOL
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 …
GENESIS – All-atom Molecular Dynamics Simulation
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 …
Finding alternate software
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, …
Docker saves the day – Roadmaps – rivem
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 …
Principios de Virología books are online
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 …
PyMOL tutorial books released
Summary: 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 …