[phenixbb] Recommendations for refining a large model against many focused maps

[vincent Chaptal]

Hi Matthias,

phenix.varref was designed to refine a series of models into a series of 
maps that are following each other, such as the ones coming from 3DVA 
(cryosparc) or multi-body refinement (Relion).
It works for very large structures like the spliceosome (2.5 MDa, 
protein+DNA chains) so it should work for you large model too. It might 
be worth testing on your system.

Varref only runs using the command line for now, and you may access it 
through the nightly builds. Dev-4933 is the latest update so anything 
stable after that will work. A doc is also accessible: 
https://phenix-online.org/documentation/reference/varref.html

Don't hesitate to contact me if you need help.
Best
Vincent

Le 30/09/2023 à 18:27, Vorländer,Matthias Kopano a écrit :
>
> Hi everyone,
>
> Apologies if this has been asked before, but I would like to know what 
> are  the recommended procedures to refine a model against many (>10) 
> cryo-EM  maps from local refinement? Some of the maps have substantial 
> overlap between them, and I manually annotated which part of the model 
> is best resolved in which map.
>
> Very grateful for any suggestions,
>
> Best wishes,
>
> Matthias
>
>
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-- 

Vincent Chaptal, PhD

Director of GdR APPICOM

Drug Resistance and Membrane Proteins Lab


MMSB -UMR5086

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.appicom.cnrs.fr

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