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<div class=""><span class="">Hi,</span></div>
<span class=""></span><span class="">
<div class=""><span class=""><br class="">
</span></div>
I am guessing what we are talking about here are the maps generated by cryoSPARC 3D variability analysis. See: </span>Punjani A & Fleet DJ (2021) 3D Variability Analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. Journal
of Structural Biology: 107702 <a href="https://doi.org/10.1016/j.jsb.2021.107702" class="">https://doi.org/10.1016/j.jsb.2021.107702</a><span class=""><br class="">
</span><span class=""><br class="">
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 <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="">
</span>Except some ideally rigid particles like apoferritin, pretty much everything shows some degree of flexibility that generates continuous heterogeneity in cryoEM images. <span class="">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.</span>
<div class=""><span class=""><br class="">
</span></div>
<div class=""><span class="">Cheers,<br class="">
<div class=""><br class="">
Guillaume<br class="">
<br class="">
</div>
<br class="">
<blockquote type="cite" class="">On 11 Jan 2022, at 17:16, Pavel Afonine <<a href="mailto:pafonine@lbl.gov" class="">pafonine@lbl.gov</a>> wrote:<br class="">
<br class="">
Hi Vincent,<br class="">
<br class="">
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!<br class="">
<br 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?<br class="">
<br class="">
Pavel<br class="">
<br class="">
On 1/11/22 01:48, vincent Chaptal wrote:<br class="">
<blockquote type="cite" cite="mid:7d57b86d-4765-2b17-b53a-4d1a270fcaba@ibcp.fr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
Hi Phenix-ers, <br class="">
<br class="">
I thought to ask for something that I believe you have already 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 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. <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 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? <br class="">
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? <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="">
<a href="http://www.appicom.cnrs.fr" class="">http://www.appicom.cnrs.fr</a><br class="">
http://mmsb.cnrs.fr/en/<br class="">
<br class="">
<br class="">
<br class="">
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