Manual model building with UCSF Chimera & Coot 0.9 (Virtual workshop held May 14th, 2020)

This is a recording of a virtual workshop on manual building/refinement of atomic models in to cryoEM density maps, using UCSF Chimera for initial fitting and COOT 0.9 for building/refinement. Click "Show More" below for PDF, data and timestamps!

The pdf used in the tutorial (which includes a link to all the required data) can be downloaded here:

https://www.dropbox.com/s/hrsi2ntatwh...

The micrographs used to generate the map are from a beautiful cryoEM dataset of hemoglobin available in EMPIAR, data generated by Mark Herzik, Mengyu Wu, and Gabe Lander: https://www.ebi.ac.uk/pdbe/emdb/empia...

Useful timestamps:
2:18 - Start of chimera
5:49 - Start rigid body fit
10:09 - Inspection of model fit
12:50 - Start COOT
16:57 - Start build helix
25:29 - Renumber helix
26:11 - Merge helix
27:09 - Assign sequence of helix
30:03 - Extend helix
31:09 - Secondary structure prediction
33:13 - Generating a threaded model
35:48 - Incorporate threaded model in COOT
39:29 - Chain refine
44:17 - Loop fitting
51:48 - Heme fitting
57:15 - Comparing with reference model
58:11 - Map postprocessing comparison
1:02:51 - COOT Scripting
1:05:03 - Q&A

Thanks for watching, hope it's helpful! Any/all feedback welcome :-)

Cheers
Oli