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

How is that different from running parallel jobs of n models against n maps? On 1/13/2022 8:17 AM, Oliver Clarke wrote:

Hi,

Just to add my two cents, I agree this would be really useful for a lot of folks. Analysis of continuously distributed variability is very common these days in cryoEM, and having a way to jointly refine an ensemble of models against a series of maps would be very handy. Cryodrgn, 3D-VA in cryosparc, ManifoldEM, multibody refinement in relion - there are many tools now for generating a series of density maps potentially corresponding to conformational modes, so having the capacity in phenix to refine models against each map would be very helpful.

Cheers Oli

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Message: 1 Date: Wed, 12 Jan 2022 10:36:27 +0100 From: vincent Chaptal To: Guillaume Gaullier , Pavel Afonine Cc: PHENIX user mailing list Subject: Re: [phenixbb] refinement of an ensemble of structures -> cryoEM variability Message-ID: Content-Type: text/plain; charset="utf-8"; Format="flowed"

Hi Guillaume,

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

Best Vincent

Le 12/01/2022 ? 10:09, Guillaume Gaullier a ?crit?:

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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

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On 11 Jan 2022, at 17:16, Pavel Afonine 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:

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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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