What is Augmented Reality? Augmented Reality (AR) is an exciting technology that overlays virtual elements on top of the real world, allowing for a unique and immersive user experience. The Apple AR platform only uses the web browser “Safari” and does not require any plug-in or specialized software, only that portable electronics (iPhone, iPad) have …
NCBI tutorial: iCn3D hands-on workshop “I see in 3D” (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode […] – (Longer description.) This workshop is designed for life scientists with some (intermediate) expertise in structural biology. The topics of structure prediction, molecular …
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 …
NOTE: this post becoming too long, its content is now moved and updated on the page: PyMOL Resources PyMOL resources Summary This post provides resources on PyMOL What is PyMOL and how to get it The University of Wisconsin participates in the licensing of PyMOL Campus wide. License and software are available on the Campus …
The Fundamentals of Biochemistry: Interactive Tutorials from Colorado State University was created by Dr. David Fahrney and edited by Ben Robinson. The 10th edition contains 10 interactive tutorials of the planned 16 chapters. Link: https://bc401.bmb.colostate.edu/ Using the javacript-based JMol web plug-in they provide easy to use, script-based interactive lessons detailing many structural aspect of biomolecules. …
Building a Protein Backbone from alpha-Carbon Files containing only C-alpha ATOM records can be the result of modeling but can also be a step in structure resolution. Theoretical models are now deposited in the ModelArchive(*). How can we obtain a complete structure for further investigation, e.g. to use in a molecular graphics software? Using Sybyl? In …
I previously wrote a small booklet using PyMOL to illustrate PyMOL scripting methods and highlight some SARS-CoV-2 (COVID-19) protein structures. (See Blog titled: Covid-19 Coloring Book and PyMOL scripts book) These protein structures are explored closely in the following movie. The video below depicts COVID-19 protein structures with a scientific, biochemistry oriented voice over text. …
Update 1: reported in the CALS eNewsletter on April 17 [Archived May 2, 2020] Update 2: I compiled a table with more Covid-19 coloring books from other inspired sources. Friday, April 10, 2020 (“Good Friday”) I have created a booklet titled “SARS-CoV-2 – COVID-19 | A Coloring Book” that parents who are spending a lot …
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 …