Summary This post is a summary of installation of AlphaFold2 onto a Macintosh with an M1 style (arm64) computer chip (i.e. not an Intel/AMD Chip.) This post started with the blog post Installing Alphafold2 on …
PyMOL
Augmented Reality of Molecules – episode 1
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 …
3D Molecular Structures Analysis with NCBI iCn3D
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.) …
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 …
PyMOL resources, books and references
NOTE: this post becoming too long, its content is now moved and updated on the page: PyMOL Resoruces PyMOL resources Summary This post provides resources on PyMOL What is PyMOL and how to get it …
The Fundamentals of Biochemistry: Interactive Tutorials
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/ …
Protein Backbone from alpha-Carbon
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(*). …
Covid-19 protein structures movie
I previously wrote a small booklet using PyMOL to illustrate PyMOL scripting methods and highlight some SARS-CoV-2 (COVID-19) protein structures. These are explored closely in the following movie. The video below depicts COVID-19 protein structures …
Covid-19 Coloring Book and PyMOL scripts book
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”) …
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.