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<font size="4"><font face="monospace">Hi Guillaume, <br>
<br>
thanks for the backup. <br>
It's exactly my feeling also. <br>
<br>
Best<br>
Vincent<br>
</font></font><br>
<div class="moz-cite-prefix">Le 12/01/2022 à 10:09, Guillaume
Gaullier a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:9604699C-C0BE-42C5-8911-342BA0D1C7C5@icm.uu.se">
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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="moz-txt-link-freetext" moz-do-not-send="true">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="moz-txt-link-freetext" moz-do-not-send="true">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="moz-txt-link-freetext" moz-do-not-send="true">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;
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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="moz-txt-link-freetext" moz-do-not-send="true">http://www.appicom.cnrs.fr</a><br
class="">
<a class="moz-txt-link-freetext" href="http://mmsb.cnrs.fr/en/">http://mmsb.cnrs.fr/en/</a><br class="">
<br class="">
<br class="">
<br class="">
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<p class="p1"><span class="s1">Vincent Chaptal, PhD</span></p>
<p class="p1"><span class="s1">Director of GdR APPICOM</span></p>
<p class="p1"><span class="s1">Drug Resistance and Membrane
Proteins Lab</span></p>
<p class="p2"><span class="s1"></span><br>
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class="Apple-converted-space"> </span></span></p>
<p class="p1"><span class="s1">69007 LYON</span></p>
<p class="p1"><span class="s1">FRANCE</span></p>
<p class="p1"><span class="s1">+33 4 37 65 29 01</span></p>
<p class="p1"><span class="s1"><a class="moz-txt-link-freetext" href="http://www.appicom.cnrs.fr">http://www.appicom.cnrs.fr</a></span></p>
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