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 with a scientific, biochemistry oriented voice over text.
Structures reviewed during the movie, with PDB code:
- 6VSB – Spike protein
- 6VW1 – RBD of the spike protein in complex with ACE2 – Angiotensin converting enzyme
- 6SGC – Rabbit ribosome stalled on a poly-A tail
- 6Y2E – SARS CoV-2 main protease
- 6Y2F – SARS CoV-2 main protease bound to an inhibitor
Close-up of structures are explored with contact or hydrogen bonding information.
Some biochemical reactions are explained in organic chemistry terms.
Many segments were animated thanks to the built-in “scenes” methods in PyMOL. Scenes are very useful in many ways, not only for creating movies, but also to create and then navigate between different representations. On that same youtube channel one video explains scenes (PyMOL: Working with Scenes.) This tutorial series is very well done and I have included the PyMOL Tutorials YouTube List at the end of the PyMOL tutorial page.