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Combining all maps from a map series from 3DVA would be equivalent to taking the "consensus" map before 3DVA was applied, I believe (it depends what one means by "combine"). This map is blurry, since it results from aligning images of particles that all have
slightly different conformations (and therefore can never align perfectly). So, doing this would cancel all the benefits of running 3DVA.
<div class=""><br class="">
</div>
<div class="">The same applies with cryoDRGN, it would not be useful to average together all the different states it found in a heterogeneous set of particles.<br class="">
<div class=""><br class="webkit-block-placeholder">
</div>
<div class="">And to answer this earlier question:</div>
<div class=""><br class="">
</div>
<div class="">
<blockquote type="cite" class="">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?</blockquote>
<br class="">
</div>
<div class="">The big picture is that <span style="-webkit-text-stroke-color: rgb(0, 0, 0); -webkit-text-stroke-width: initial;" class="">3DVA is a PCA trying to find the major ways in which 2D particle images differ. Once principal components of variability
are identified, it can then generate maps that are linear interpolations between observed particles, taken along the principal components. What is most often done in practice is to generate a series of maps traversing the first one or two principal components
(or as many as you want until you explain most of the variability in the data). This can often identify hinge motions in a complex, or similar large-scale conformational changes. Now, because these maps are linear interpolations, they can sometimes show unphysical
features, so I am not sure refining a model against these maps would work well. But it would with maps from cryoDRGN, since it does no such interpolation and can even generate maps that are guaranteed to be supported by observed data.</span></div>
<div class=""><span style="-webkit-text-stroke-color: rgb(0, 0, 0); -webkit-text-stroke-width: initial;" class=""><br class="">
</span></div>
<div class=""><span style="-webkit-text-stroke-color: rgb(0, 0, 0); -webkit-text-stroke-width: initial;" class="">This is very simplified, I am no expert in computational methods. If you want to understand better what is reasonable to do with these maps, you
need to know how they are produced, and the two papers I pointed to in my previous message explain this in detail.</span></div>
<div class=""><span style="-webkit-text-stroke-color: rgb(0, 0, 0); -webkit-text-stroke-width: initial;" class=""><br class="">
</span></div>
<div class=""><span style="-webkit-text-stroke-color: rgb(0, 0, 0); -webkit-text-stroke-width: initial;" class="">I hope this helps,</span></div>
<div class="">
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<br class="Apple-interchange-newline">
Guillaume</div>
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<br class="">
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</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 13 Jan 2022, at 17:40, Pavel Afonine <<a href="mailto:pafonine@lbl.gov" class="">pafonine@lbl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Hi,<br class="">
<br class="">
good discussion, thanks!<br class="">
<br class="">
Instead of having a series of maps would it make sense to combine all these maps into one composite map, and then refine one atomic model against this composite map, and model variability using alternative conformations (very much like in crystallography)?<br class="">
<br class="">
If that's a possible route then all is needed is a tool to combine the maps and phenix.real_space_refine can already handle models with alternative conformations (can refine occupancies in real space).<br class="">
<br class="">
Pavel<br class="">
<br class="">
On 1/13/22 08:17, Oliver Clarke wrote:<br class="">
<blockquote type="cite" class="">Hi,<br class="">
<br class="">
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.<br class="">
<br class="">
Cheers<br class="">
Oli<br class="">
<br class="">
<blockquote type="cite" class=""><br class="">
Message: 1<br class="">
Date: Wed, 12 Jan 2022 10:36:27 +0100<br class="">
From: vincent Chaptal <<a href="mailto:vincent.chaptal@ibcp.fr" class="">vincent.chaptal@ibcp.fr</a>><br class="">
To: Guillaume Gaullier <<a href="mailto:guillaume.gaullier@icm.uu.se" class="">guillaume.gaullier@icm.uu.se</a>>,<span class="Apple-tab-span" style="white-space:pre">
</span>Pavel Afonine<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><<a href="mailto:pafonine@lbl.gov" class="">pafonine@lbl.gov</a>><br class="">
Cc: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org" class="">phenixbb@phenix-online.org</a>><br class="">
Subject: Re: [phenixbb] refinement of an ensemble of structures -><br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>cryoEM variability<br class="">
Message-ID: <<a href="mailto:ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3@ibcp.fr" class="">ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3@ibcp.fr</a>><br class="">
Content-Type: text/plain; charset="utf-8"; Format="flowed"<br class="">
<br class="">
Hi Guillaume,<br class="">
<br class="">
thanks for the backup.<br class="">
It's exactly my feeling also.<br class="">
<br class="">
Best<br class="">
Vincent<br class="">
<br class="">
Le 12/01/2022 ? 10:09, Guillaume Gaullier a ?crit?:<br class="">
<blockquote type="cite" class="">Hi,<br class="">
<br class="">
I am guessing what we are talking about here are the maps generated by<br class="">
cryoSPARC 3D variability analysis. See: Punjani A & Fleet DJ (2021) 3D<br class="">
Variability Analysis: Resolving continuous flexibility and discrete<br class="">
heterogeneity from single particle cryo-EM.?Journal of Structural<br class="">
Biology: 107702 <a href="https://doi.org/10.1016/j.jsb.2021.107702" class="">https://doi.org/10.1016/j.jsb.2021.107702</a><br class="">
<br class="">
But this is not the only program that generates series of maps to<br class="">
describe continuous heterogeneity from single-particle cryoEM images,<br class="">
see also cryoDRGN:?Zhong ED, Bepler T, Berger B & Davis JH (2021)<br class="">
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using<br class="">
neural networks.?Nature Methods: 1?10<br class="">
<a href="https://doi.org/10.1038/s41592-020-01049-4" class="">https://doi.org/10.1038/s41592-020-01049-4</a><br class="">
<br class="">
Except some ideally rigid particles like apoferritin, pretty much<br class="">
everything shows some degree of flexibility that generates continuous<br class="">
heterogeneity in cryoEM images. So, my feeling is that a user-friendly<br class="">
program to fit a series of models (ideally, auto-generated from a<br class="">
single starting model) to a map series is probably going to be a<br class="">
standard requirement pretty soon for typical single-particle cryoEM<br class="">
projects.<br class="">
<br class="">
Cheers,<br class="">
<br class="">
Guillaume<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On 11 Jan 2022, at 17:16, Pavel Afonine <pafonine@lbl.gov> wrote:<br class="">
<br class="">
Hi Vincent,<br class="">
<br class="">
this looks like a very specialized task that I've never heard of<br class="">
before! We can add a tool to do that if this becomes something that<br class="">
more than one person does more than once. Meanwhile, a simple script<br class="">
in a language of your?preference (python, linux shell, etc) should do<br class="">
the job. I can help with a script if needed, let me know!<br class="">
<br class="">
Also.. just curious -- what is "3D variability of this map"? Is this<br class="">
one map that is a composition of several map or an ensemble of maps?<br class="">
<br class="">
Pavel<br class="">
<br class="">
On 1/11/22 01:48, vincent Chaptal wrote:<br class="">
<blockquote type="cite" class="">Hi Phenix-ers,<br class="">
<br class="">
I thought to ask for something that I believe you have already<br class="">
implemented, but I'm not sure of the best tool to use.<br class="">
<br class="">
I have a cryoEM map where I refine my "high resolution" structure. I<br class="">
also have the 3D variability of this map that shows?several maps<br class="">
varying around the consensus high-res map. I want to refine an<br class="">
ensemble (20) of structures, one for every 20?maps around the<br class="">
consensus map.<br class="">
Is there a tool in phenix to do this?<br class="">
<br class="">
I could refine individually the high-res structure into each map<br class="">
incrementally; since every map differs a little from the?original<br class="">
one, Real-space-refinement could move the structure a little at a<br class="">
time. Then I could combine all the PDBs in an?ensemble?<br class="">
A tool to refine variability would be very useful. Input could be a<br class="">
PDB and an ensemble of maps, and output would be all the?PDBs combined?<br class="">
<br class="">
Thank you.<br class="">
<br class="">
All the best<br class="">
Vincent<br class="">
<br class="">
<br class="">
-- <br class="">
Vincent Chaptal, PhD<br class="">
Director of GdR APPICOM<br class="">
Drug Resistance and Membrane Proteins Lab<br class="">
<br class="">
MMSB -UMR5086<br class="">
7 passage du Vercors<br class="">
69007 LYON<br class="">
FRANCE<br class="">
+33 4 37 65 29 01<br class="">
http://www.appicom.cnrs.fr<br class="">
http://mmsb.cnrs.fr/en/<br class="">
<br class="">
<br class="">
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Page Title<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
N?r du har kontakt med oss p? Uppsala universitet med e-post s?<br class="">
inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om<br class="">
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<br class="">
Director of GdR APPICOM<br class="">
<br class="">
Drug Resistance and Membrane Proteins Lab<br class="">
<br class="">
<br class="">
MMSB -UMR5086<br class="">
<br class="">
7 passage du Vercors<br class="">
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69007 LYON<br class="">
<br class="">
FRANCE<br class="">
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Message: 2<br class="">
Date: Wed, 12 Jan 2022 18:11:02 +0530<br class="">
From: Viney Singh <vineysingh22@gmail.com><br class="">
To: phenixbb@phenix-online.org<br class="">
Subject: [phenixbb] regarding number of unique reflections<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><CALO_hTx1dtmm2nfkd4+9iPUb+jmAq4kM2ObB=jwrQ5VvCuUTmQ@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear all,<br class="">
<br class="">
First of all sorry for the novice question.<br class="">
<br class="">
I *processed* one of my datasets using xds. Since I was not expecting an<br class="">
anomalous signal, I kept Friedel's Law = True.<br class="">
The number of unique reflections I got: *17,000*<br class="">
I used xds_ASCII.HKL after correct.LP and converted it to mtz using Phenix<br class="">
with 10% reflections for Rfree calculations.<br class="">
<br class="">
Now, when I am trying to* refine *the structure in Phenix, the structure is<br class="">
being refined against *32,300* reflections with *3230* reflections for<br class="">
Rfree calculation. Looks like refinement is treating Friedel's pair as two<br class="">
different reflections.<br class="">
<br class="">
When I am trying to upload PDB on rcsb, on the refinement tab, the number<br class="">
of reflections used for refinement and Rfree calculations are shown as<br class="">
32,300 and 3220 respectively, while in the validation report, no. of<br class="">
reflections used for Rfree calculation are shown as *1700*.<br class="">
<br class="">
I would really appreciate if someone can guide me to resolve this<br class="">
discrepancy.<br class="">
<br class="">
Thanks in advance.<br class="">
<br class="">
Viney<br class="">
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<br class="">
Message: 3<br class="">
Date: Wed, 12 Jan 2022 15:03:49 +0000<br class="">
From: "Tanner, John J." <TannerJJ@missouri.edu><br class="">
To: Viney Singh <vineysingh22@gmail.com>, "phenixbb@phenix-online.org"<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><phenixbb@phenix-online.org><br class="">
Subject: Re: [phenixbb] regarding number of unique reflections<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><CH0PR01MB7154E88CABD14AE39C4FD543A7529@CH0PR01MB7154.prod.exchangelabs.com><br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><br class="">
Content-Type: text/plain; charset="us-ascii"<br class="">
<br class="">
This is a common problem. I use ccp4i CAD to remove all the columns from the .mtz file except for F, SIGF, and FreeR_flag, and then use this new .mtz file in refinement before depositing. For the next structure, remember to do this in the early stages.<br class="">
<br class="">
--<br class="">
John J. Tanner<br class="">
Professor of Biochemistry and Chemistry<br class="">
Associate Chair of Biochemistry<br class="">
Department of Biochemistry<br class="">
University of Missouri<br class="">
117 Schweitzer Hall<br class="">
503 S College Avenue<br class="">
Columbia, MO 65211<br class="">
Phone: 573-884-1280<br class="">
Email: tannerjj@missouri.edu<mailto:tannerjj@missouri.edu><br class="">
https://cafnrfaculty.missouri.edu/tannerlab/<br class="">
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C<br class="">
Office: Schlundt Annex 203A<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
From: phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Viney Singh <vineysingh22@gmail.com><br class="">
Date: Wednesday, January 12, 2022 at 6:52 AM<br class="">
To: phenixbb@phenix-online.org <phenixbb@phenix-online.org><br class="">
Subject: [phenixbb] regarding number of unique reflections<br class="">
WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.<br class="">
Dear all,<br class="">
<br class="">
First of all sorry for the novice question.<br class="">
<br class="">
I processed one of my datasets using xds. Since I was not expecting an anomalous signal, I kept Friedel's Law = True.<br class="">
The number of unique reflections I got: 17,000<br class="">
I used xds_ASCII.HKL after correct.LP and converted it to mtz using Phenix with 10% reflections for Rfree calculations.<br class="">
<br class="">
Now, when I am trying to refine the structure in Phenix, the structure is being refined against 32,300 reflections with 3230 reflections for Rfree calculation. Looks like refinement is treating Friedel's pair as two different reflections.<br class="">
<br class="">
When I am trying to upload PDB on rcsb, on the refinement tab, the number of reflections used for refinement and Rfree calculations are shown as 32,300 and 3220 respectively, while in the validation report, no. of reflections used for Rfree calculation are
shown as 1700.<br class="">
<br class="">
I would really appreciate if someone can guide me to resolve this discrepancy.<br class="">
<br class="">
Thanks in advance.<br class="">
<br class="">
Viney<br class="">
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Message: 4<br class="">
Date: Wed, 12 Jan 2022 21:28:37 +0530<br class="">
From: Viney Singh <vineysingh22@gmail.com><br class="">
To: "Tanner, John J." <TannerJJ@missouri.edu><br class="">
Cc: "phenixbb@phenix-online.org" <phenixbb@phenix-online.org><br class="">
Subject: Re: [phenixbb] regarding number of unique reflections<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><CALO_hTyJj3bSg_rev1hZVEvr=K91+C9x1AtbdrpiOajsSKk-Hg@mail.gmail.com><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Thanks a lot, Dr .Tanner. I will try the suggestion. Currently, I tried<br class="">
running xds_ASCII.HKL on pointless followed by truncate. Seems like mtz is<br class="">
now all good. But I am wondering if this is the right way to go about it?<br class="">
<br class="">
<br class="">
<br class="">
On Wed, Jan 12, 2022 at 8:33 PM Tanner, John J. <TannerJJ@missouri.edu><br class="">
wrote:<br class="">
<br class="">
<blockquote type="cite" class="">This is a common problem. I use ccp4i CAD to remove all the columns from<br class="">
the .mtz file except for F, SIGF, and FreeR_flag, and then use this new<br class="">
.mtz file in refinement before depositing. For the next structure, remember<br class="">
to do this in the early stages.<br class="">
<br class="">
<br class="">
<br class="">
--<br class="">
<br class="">
John J. Tanner<br class="">
<br class="">
Professor of Biochemistry and Chemistry<br class="">
<br class="">
Associate Chair of Biochemistry<br class="">
<br class="">
Department of Biochemistry<br class="">
<br class="">
University of Missouri<br class="">
117 Schweitzer Hall<br class="">
<br class="">
503 S College Avenue<br class="">
Columbia, MO 65211<br class="">
Phone: 573-884-1280<br class="">
<br class="">
Email: tannerjj@missouri.edu <tannerjj@missouri.edu><br class="">
https://cafnrfaculty.missouri.edu/tannerlab/<br class="">
<br class="">
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C<br class="">
<br class="">
Office: Schlundt Annex 203A<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
*From: *phenixbb-bounces@phenix-online.org <<br class="">
phenixbb-bounces@phenix-online.org> on behalf of Viney Singh <<br class="">
vineysingh22@gmail.com><br class="">
*Date: *Wednesday, January 12, 2022 at 6:52 AM<br class="">
*To: *phenixbb@phenix-online.org <phenixbb@phenix-online.org><br class="">
*Subject: *[phenixbb] regarding number of unique reflections<br class="">
<br class="">
*WARNING:* This message has originated from an External Source. This may<br class="">
be a phishing expedition that can result in unauthorized access to our IT<br class="">
System. Please use proper judgment and caution when opening attachments,<br class="">
clicking links, or responding to this email.<br class="">
<br class="">
Dear all,<br class="">
<br class="">
<br class="">
<br class="">
First of all sorry for the novice question.<br class="">
<br class="">
<br class="">
<br class="">
I *processed* one of my datasets using xds. Since I was not expecting an<br class="">
anomalous signal, I kept Friedel's Law = True.<br class="">
<br class="">
The number of unique reflections I got: *17,000*<br class="">
<br class="">
I used xds_ASCII.HKL after correct.LP and converted it to mtz using Phenix<br class="">
with 10% reflections for Rfree calculations.<br class="">
<br class="">
<br class="">
<br class="">
Now, when I am trying to* refine *the structure in Phenix, the structure<br class="">
is being refined against *32,300* reflections with *3230* reflections for<br class="">
Rfree calculation. Looks like refinement is treating Friedel's pair as two<br class="">
different reflections.<br class="">
<br class="">
<br class="">
<br class="">
When I am trying to upload PDB on rcsb, on the refinement tab, the number<br class="">
of reflections used for refinement and Rfree calculations are shown as<br class="">
32,300 and 3220 respectively, while in the validation report, no. of<br class="">
reflections used for Rfree calculation are shown as *1700*.<br class="">
<br class="">
<br class="">
<br class="">
I would really appreciate if someone can guide me to resolve this<br class="">
discrepancy.<br class="">
<br class="">
<br class="">
<br class="">
Thanks in advance.<br class="">
<br class="">
<br class="">
<br class="">
Viney<br class="">
<br class="">
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