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

[vincent Chaptal]

Hi Guillaume,

thanks for the backup.
It's exactly my feeling also.

Best
Vincent

Le 12/01/2022 à 10:09, Guillaume Gaullier a écrit :
> Hi,
>
> I am guessing what we are talking about here are the maps generated by 
> cryoSPARC 3D variability analysis. See: Punjani A & Fleet DJ (2021) 3D 
> Variability Analysis: Resolving continuous flexibility and discrete 
> heterogeneity from single particle cryo-EM. Journal of Structural 
> Biology: 107702 https://doi.org/10.1016/j.jsb.2021.107702
>
> But this is not the only program that generates series of maps to 
> describe continuous heterogeneity from single-particle cryoEM images, 
> see also cryoDRGN: Zhong ED, Bepler T, Berger B & Davis JH (2021) 
> CryoDRGN: reconstruction of heterogeneous cryo-EM structures using 
> neural networks. Nature Methods: 1–10 
> https://doi.org/10.1038/s41592-020-01049-4
>
> Except some ideally rigid particles like apoferritin, pretty much 
> everything shows some degree of flexibility that generates continuous 
> heterogeneity in cryoEM images. So, my feeling is that a user-friendly 
> program to fit a series of models (ideally, auto-generated from a 
> single starting model) to a map series is probably going to be a 
> standard requirement pretty soon for typical single-particle cryoEM 
> projects.
>
> Cheers,
>
> Guillaume
>
>
>> On 11 Jan 2022, at 17:16, Pavel Afonine <pafonine at lbl.gov> wrote:
>>
>> 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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-- 

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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