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 is a Python library for building and manipulating protein molecular structures. From an amino acid sequence the user can create …
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 later made available by the Qutemol software, unfortunately not updated since 2007 and therefore no longer working on many systems, …
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 sessions. NCBI Outreach Events The National Center for Biotechnology Information (NCBI) is a division of the National Library of Medicine …
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 this is easy, it is not the “best way” to use PyMOL if one wants to be able to reproduce …
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 offto turn it off.) The alternative is to use the menu cascade: Display > Stereo. However, there are 2 ways …
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 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 …
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 this blog I will share memories and stories, images and perhaps (probably useless) software code… as often people ask me …
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 …