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

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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:
www.dropbox.co...
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: www.ebi.ac.uk/...
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

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12 сен 2024

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Комментарии : 11

@AmazingIsScience 4 года назад

Thanks a lot for sharing the great stuff! I have been self-studying coot model building for several months but still confused. Your video and tutorial are very helpful! Looking forward to more virtual workshop from you.

@AGthe7 4 года назад

Thanks Oli for your Chimera and Coot tutorial, it is of great help! =D I am currently on my first structural biology project,and I lack not only the background knowledge, but I am also very alone and not many people around me know Cryo-EM and model building. This came really in good help, THANK YOU =)

@olibclarke 4 года назад

Thanks Andre, glad it was helpful!! :-)

@AGthe7 4 года назад

@@olibclarke tried to message on Twitter before, but it didn't work.

@md.gaziulislam9558 3 года назад

Hi !! Oli. It is finally a great video for everyone I think. you were too fast but thanks for your nice presentation. I am going to use Coot.

@vamseedharr 3 года назад

Hi Oli, Thank you for this video. Very helpful. You talked about building (or not) into loops which have poor density. How do you approach molecules that have symmetry and one or two of the subunits have density in a particular loop but the third doesn't? Do you still build into the 3rd one too or leave it alone? Thanks

@RavindraThakkar369 2 года назад

nice tutorial. Can you please explain me how you installed coot within chimera?

@asgarabbaskazrani4391 4 года назад

many thanks for the video, I am curious why coot mode is an unrecognised command when I am using it?

@yongmeiliu8730 4 года назад

Thanks Oli , I'm new to build models.Could you give me some advice like what kind of books or knowledge should be known to get building models easier ?

@yongmeiliu8730 4 года назад

It's still very difficult for me to understand what you did in coot.

@anna-sophieschlemmer4332 3 года назад

great tutorial, great script! I am running into an error when I merge>chain: no can do, chain must be in the same mol and have non-overlapping ranges. I have used merge>mol before merge>chain but it still gives me the error. anything I am missing here or is there another way to create a bond between two molecules?