[phenixbb] refinement of an ensemble of structures -> cryoEM variability

[Pavel Afonine]

Hi Vincent,

this looks like a very specialized task that I've never heard of before! 
We can add a tool to do that if this becomes something that more than 
one person does more than once. Meanwhile, a simple script in a language 
of your preference (python, linux shell, etc) should do the job. I can 
help with a script if needed, let me know!

Also.. just curious -- what is "3D variability of this map"? Is this one 
map that is a composition of several map or an ensemble of maps?

Pavel

On 1/11/22 01:48, vincent Chaptal wrote:
> Hi Phenix-ers,
>
> I thought to ask for something that I believe you have already 
> implemented, but I'm not sure of the best tool to use.
>
> I have a cryoEM map where I refine my "high resolution" structure. I 
> also have the 3D variability of this map that shows several maps 
> varying around the consensus high-res map. I want to refine an 
> ensemble (20) of structures, one for every 20 maps around the 
> consensus map.
> Is there a tool in phenix to do this?
>
> I could refine individually the high-res structure into each map 
> incrementally; since every map differs a little from the original one, 
> Real-space-refinement could move the structure a little at a time. 
> Then I could combine all the PDBs in an ensemble?
> A tool to refine variability would be very useful. Input could be a 
> PDB and an ensemble of maps, and output would be all the PDBs combined?
>
> Thank you.
>
> All the best
> Vincent
>
>
> -- 
>
> 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
>
> http://mmsb.cnrs.fr/en/
>
>
>
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