Summary Pose is a Python library for building and manipulating protein molecular structures. Builds with L- and D- amino acids or a mixture; can open existing PDB structures. Computes many molecular properties. Pose Library Pose …
Molecular Graphics
3D Protein Imager a PyMOL/Qutemol web alternative
Summary Molecule of the Month In the year 2000 David Goodsell started to provide stories on the The Protein Data Bank web site as the “molecule of the month” with his unique style that was …
NCBI-Workshops
Summary The National Center for Biotechnology Information (NCBI) offers events, including workshops hands-on, interactive training sessions. All events are listed on the NCBI Outreach Events page. Workshop recordings and materials remain available after the live …
Faster image creation in PyMOL: Shortcuts and Docker
Summary PyMOL command scripts are available natively and within Docker images. PyMOL Scripts PyMOL offers a very easy-to-use graphical user interface (GUI) to manipulate loaded molecule, and alter the appearance and coloring options. However, while …
PyMOL Stereo viewing
PyMOL Stereo viewing PyMOL can display stereo in many ways. Unless special equipment is available, the method is to split the PyMOL 3D view area in two with the command stereo on (and stereo …
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 …
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 …
33 years at UW-Madison
Blog series This June 2019 marked my 33 years at UW-Madison when I joined Prof. Paul Kaesberg‘s lab as a PostDoc to learn the then new methods of “cloning and sequencing” (i.e. Sanger sequencing.) 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 …