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

Hi, the maps are derived from an already "refined" set of particles that show homogeneity. Within this homegenity still lies some heterogeneity, which has some continuum, hence continuous heterogeneity. Thus, I don't think combining the maps will not work as it will result in most cases as a big blob. In my mind, the best reconstruction lies more or less at the center of a gaussian of particle distribution (also because it is a prior of such a job!). So, if there are 20 maps output from the job, then I would take the model built on the consensus map, and refine against map 10. output of map 10 would be refined against 11. output of 11 against 12, etc... (same thing going down from 9 to 0). The idea behind it is that there is a sequence of events, this sequence shows a bit more deviation from the center of the gaussian. And since the variation is not huge, my guess is that a standart refinement would be able to perturb enough to drive the model into the new map. Vincent Le 13/01/2022 à 18:53, Oliver Clarke a écrit :

I guess it isn't all that different.

If you run all jobs naively starting from a single model corresponding to the overall reconstruction, depending on the magnitude of the conformational changes the maps at either end of the series may be outside the radius of convergence of phenix.real_space_refine (with default parameters).

Some way to initially perturb a single model to more-or-less match the series of maps would be useful (maybe morphing in real_space_refine will already work for this?). This could probably be scripted, but having it built into phenix would be useful I think.

Oli

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Date: Thu, 13 Jan 2022 09:26:50 -0800 From: James Holton To:[email protected] Subject: Re: [phenixbb] refinement of an ensemble of structures -> cryoEM variability Message-ID:<[email protected]> Content-Type: text/plain; charset=UTF-8; format=flowed

How is that different from running parallel jobs of n models against n maps?

On 1/13/2022 8:17 AM, Oliver Clarke wrote:

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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: 107702https://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: > 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/ > > > > _______________________________________________ > phenixbb mailing list > > [email protected] > http://phenix-online.org/mailman/listinfo/phenixbb > > Unsubscribe: > [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe:[email protected] Page Title

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