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<font size="4"><font face="monospace">Hi, <br>
<br>
the maps are derived from an already "refined" set of particles
that show homogeneity. Within this homegenity </font></font><font
size="4"><font face="monospace">still </font></font><font
size="4"><font face="monospace">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. <br>
<br>
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. <br>
<br>
Vincent<br>
<br>
</font></font><br>
<div class="moz-cite-prefix">Le 13/01/2022 à 18:53, Oliver Clarke a
écrit :<br>
</div>
<blockquote type="cite"
cite="mid:24AF588E-BD9A-47D7-AACD-09F1BFD2A817@gmail.com">
<pre class="moz-quote-pre" wrap="">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
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">Date: Thu, 13 Jan 2022 09:26:50 -0800
From: James Holton <a class="moz-txt-link-rfc2396E" href="mailto:jmholton@lbl.gov"><jmholton@lbl.gov></a>
To: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
Subject: Re: [phenixbb] refinement of an ensemble of structures ->
cryoEM variability
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:92b5f0e3-c4b1-59f9-1c38-50fffcda0bb1@lbl.gov"><92b5f0e3-c4b1-59f9-1c38-50fffcda0bb1@lbl.gov></a>
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:
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">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
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">
Message: 1
Date: Wed, 12 Jan 2022 10:36:27 +0100
From: vincent Chaptal <a class="moz-txt-link-rfc2396E" href="mailto:vincent.chaptal@ibcp.fr"><vincent.chaptal@ibcp.fr></a>
To: Guillaume Gaullier <a class="moz-txt-link-rfc2396E" href="mailto:guillaume.gaullier@icm.uu.se"><guillaume.gaullier@icm.uu.se></a>, Pavel Afonine
<a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a>
Cc: PHENIX user mailing list <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
Subject: Re: [phenixbb] refinement of an ensemble of structures ->
cryoEM variability
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3@ibcp.fr"><ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3@ibcp.fr></a>
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?:
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">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 <a class="moz-txt-link-freetext" href="https://doi.org/10.1016/j.jsb.2021.107702">https://doi.org/10.1016/j.jsb.2021.107702</a>
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 class="moz-txt-link-freetext" href="https://doi.org/10.1038/s41592-020-01049-4">https://doi.org/10.1038/s41592-020-01049-4</a>
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
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">On 11 Jan 2022, at 17:16, Pavel Afonine <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a> 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:
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">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
<a class="moz-txt-link-freetext" href="http://www.appicom.cnrs.fr">http://www.appicom.cnrs.fr</a>
<a class="moz-txt-link-freetext" href="http://mmsb.cnrs.fr/en/">http://mmsb.cnrs.fr/en/</a>
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<pre class="moz-quote-pre" wrap="">Page Title
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inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om
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</pre>
</blockquote>
<pre class="moz-quote-pre" wrap="">--
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
<a class="moz-txt-link-freetext" href="http://www.appicom.cnrs.fr">http://www.appicom.cnrs.fr</a>
<a class="moz-txt-link-freetext" href="http://mmsb.cnrs.fr/en/">http://mmsb.cnrs.fr/en/</a>
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Message: 2
Date: Wed, 12 Jan 2022 18:11:02 +0530
From: Viney Singh <a class="moz-txt-link-rfc2396E" href="mailto:vineysingh22@gmail.com"><vineysingh22@gmail.com></a>
To: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
Subject: [phenixbb] regarding number of unique reflections
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Dear all,
First of all sorry for the novice question.
I *processed* one of my datasets using xds. Since I was not expecting an
anomalous signal, I kept Friedel's Law = True.
The number of unique reflections I got: *17,000*
I used xds_ASCII.HKL after correct.LP and converted it to mtz using Phenix
with 10% reflections for Rfree calculations.
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.
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*.
I would really appreciate if someone can guide me to resolve this
discrepancy.
Thanks in advance.
Viney
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Message: 3
Date: Wed, 12 Jan 2022 15:03:49 +0000
From: "Tanner, John J." <a class="moz-txt-link-rfc2396E" href="mailto:TannerJJ@missouri.edu"><TannerJJ@missouri.edu></a>
To: Viney Singh <a class="moz-txt-link-rfc2396E" href="mailto:vineysingh22@gmail.com"><vineysingh22@gmail.com></a>, <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org">"phenixbb@phenix-online.org"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
Subject: Re: [phenixbb] regarding number of unique reflections
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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.
--
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: <a class="moz-txt-link-abbreviated" href="mailto:tannerjj@missouri.edu">tannerjj@missouri.edu</a><a class="moz-txt-link-rfc2396E" href="mailto:tannerjj@missouri.edu"><mailto:tannerjj@missouri.edu></a>
<a class="moz-txt-link-freetext" href="https://cafnrfaculty.missouri.edu/tannerlab/">https://cafnrfaculty.missouri.edu/tannerlab/</a>
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A
From: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a> <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb-bounces@phenix-online.org"><phenixbb-bounces@phenix-online.org></a> on behalf of Viney Singh <a class="moz-txt-link-rfc2396E" href="mailto:vineysingh22@gmail.com"><vineysingh22@gmail.com></a>
Date: Wednesday, January 12, 2022 at 6:52 AM
To: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a> <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
Subject: [phenixbb] regarding number of unique reflections
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.
Dear all,
First of all sorry for the novice question.
I processed one of my datasets using xds. Since I was not expecting an anomalous signal, I kept Friedel's Law = True.
The number of unique reflections I got: 17,000
I used xds_ASCII.HKL after correct.LP and converted it to mtz using Phenix with 10% reflections for Rfree calculations.
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.
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.
I would really appreciate if someone can guide me to resolve this discrepancy.
Thanks in advance.
Viney
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Message: 4
Date: Wed, 12 Jan 2022 21:28:37 +0530
From: Viney Singh <a class="moz-txt-link-rfc2396E" href="mailto:vineysingh22@gmail.com"><vineysingh22@gmail.com></a>
To: "Tanner, John J." <a class="moz-txt-link-rfc2396E" href="mailto:TannerJJ@missouri.edu"><TannerJJ@missouri.edu></a>
Cc: <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org">"phenixbb@phenix-online.org"</a> <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
Subject: Re: [phenixbb] regarding number of unique reflections
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Thanks a lot, Dr .Tanner. I will try the suggestion. Currently, I tried
running xds_ASCII.HKL on pointless followed by truncate. Seems like mtz is
now all good. But I am wondering if this is the right way to go about it?
On Wed, Jan 12, 2022 at 8:33 PM Tanner, John J. <a class="moz-txt-link-rfc2396E" href="mailto:TannerJJ@missouri.edu"><TannerJJ@missouri.edu></a>
wrote:
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">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.
--
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: <a class="moz-txt-link-abbreviated" href="mailto:tannerjj@missouri.edu">tannerjj@missouri.edu</a> <a class="moz-txt-link-rfc2396E" href="mailto:tannerjj@missouri.edu"><tannerjj@missouri.edu></a>
<a class="moz-txt-link-freetext" href="https://cafnrfaculty.missouri.edu/tannerlab/">https://cafnrfaculty.missouri.edu/tannerlab/</a>
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A
*From: *phenixbb-bounces@phenix-online.org <
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>> on behalf of Viney Singh <
<a class="moz-txt-link-abbreviated" href="mailto:vineysingh22@gmail.com">vineysingh22@gmail.com</a>>
*Date: *Wednesday, January 12, 2022 at 6:52 AM
*To: *phenixbb@phenix-online.org <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
*Subject: *[phenixbb] regarding number of unique reflections
*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.
Dear all,
First of all sorry for the novice question.
I *processed* one of my datasets using xds. Since I was not expecting an
anomalous signal, I kept Friedel's Law = True.
The number of unique reflections I got: *17,000*
I used xds_ASCII.HKL after correct.LP and converted it to mtz using Phenix
with 10% reflections for Rfree calculations.
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.
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*.
I would really appreciate if someone can guide me to resolve this
discrepancy.
Thanks in advance.
Viney
</pre>
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------------------------------
Message: 4
Date: Thu, 13 Jan 2022 09:42:52 -0800
From: Pavel Afonine <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a>
To: James Holton <a class="moz-txt-link-rfc2396E" href="mailto:jmholton@lbl.gov"><jmholton@lbl.gov></a>, <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
Subject: Re: [phenixbb] refinement of an ensemble of structures ->
cryoEM variability
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</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">How is that different from running parallel jobs of n models against n
maps?
</pre>
</blockquote>
<pre class="moz-quote-pre" wrap="">
For this you need to know how to write programs/scripts (I know you do
know!). Then make sure programs down the road can handle multi-model
files (in Phenix we can read/write them but that's pretty much it).
If you have one map and one model (with altlocs) then you can just use
phenix.real_space_refine as is.
Otherwise yes, you can refine n models against n maps, in parallel or
sequentially!
Pavel
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">
On 1/13/2022 8:17 AM, Oliver Clarke wrote:
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">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
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">
Message: 1
Date: Wed, 12 Jan 2022 10:36:27 +0100
From: vincent Chaptal <a class="moz-txt-link-rfc2396E" href="mailto:vincent.chaptal@ibcp.fr"><vincent.chaptal@ibcp.fr></a>
To: Guillaume Gaullier <a class="moz-txt-link-rfc2396E" href="mailto:guillaume.gaullier@icm.uu.se"><guillaume.gaullier@icm.uu.se></a>,??? Pavel Afonine
????<a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a>
Cc: PHENIX user mailing list <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
Subject: Re: [phenixbb] refinement of an ensemble of structures ->
????cryoEM variability
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3@ibcp.fr"><ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3@ibcp.fr></a>
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Hi Guillaume,
thanks for the backup.
It's exactly my feeling also.
Best
Vincent
Le 12/01/2022 ? 10:09, Guillaume Gaullier a ?crit?:
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">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 <a class="moz-txt-link-freetext" href="https://doi.org/10.1016/j.jsb.2021.107702">https://doi.org/10.1016/j.jsb.2021.107702</a>
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 class="moz-txt-link-freetext" href="https://doi.org/10.1038/s41592-020-01049-4">https://doi.org/10.1038/s41592-020-01049-4</a>
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
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">On 11 Jan 2022, at 17:16, Pavel Afonine <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a> 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:
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">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
<a class="moz-txt-link-freetext" href="http://www.appicom.cnrs.fr">http://www.appicom.cnrs.fr</a>
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<pre class="moz-quote-pre" wrap="">--
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
<a class="moz-txt-link-freetext" href="http://www.appicom.cnrs.fr">http://www.appicom.cnrs.fr</a>
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Message: 2
Date: Wed, 12 Jan 2022 18:11:02 +0530
From: Viney Singh <a class="moz-txt-link-rfc2396E" href="mailto:vineysingh22@gmail.com"><vineysingh22@gmail.com></a>
To: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
Subject: [phenixbb] regarding number of unique reflections
Message-ID:
????<a class="moz-txt-link-rfc2396E" href="mailto:CALO_hTx1dtmm2nfkd4+9iPUb+jmAq4kM2ObB=jwrQ5VvCuUTmQ@mail.gmail.com"><CALO_hTx1dtmm2nfkd4+9iPUb+jmAq4kM2ObB=jwrQ5VvCuUTmQ@mail.gmail.com></a>
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Dear all,
First of all sorry for the novice question.
I *processed* one of my datasets using xds. Since I was not
expecting an
anomalous signal, I kept Friedel's Law = True.
The number of unique reflections I got: *17,000*
I used xds_ASCII.HKL after correct.LP and converted it to mtz using
Phenix
with 10% reflections for Rfree calculations.
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.
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*.
I would really appreciate if someone can guide me to resolve this
discrepancy.
Thanks in advance.
Viney
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------------------------------
Message: 3
Date: Wed, 12 Jan 2022 15:03:49 +0000
From: "Tanner, John J." <a class="moz-txt-link-rfc2396E" href="mailto:TannerJJ@missouri.edu"><TannerJJ@missouri.edu></a>
To: Viney Singh <a class="moz-txt-link-rfc2396E" href="mailto:vineysingh22@gmail.com"><vineysingh22@gmail.com></a>, <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org">"phenixbb@phenix-online.org"</a>
????<a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
Subject: Re: [phenixbb] regarding number of unique reflections
Message-ID:
????<a class="moz-txt-link-rfc2396E" href="mailto:CH0PR01MB7154E88CABD14AE39C4FD543A7529@CH0PR01MB7154.prod.exchangelabs.com"><CH0PR01MB7154E88CABD14AE39C4FD543A7529@CH0PR01MB7154.prod.exchangelabs.com></a>
Content-Type: text/plain; charset="us-ascii"
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.
--
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: <a class="moz-txt-link-abbreviated" href="mailto:tannerjj@missouri.edu">tannerjj@missouri.edu</a><a class="moz-txt-link-rfc2396E" href="mailto:tannerjj@missouri.edu"><mailto:tannerjj@missouri.edu></a>
<a class="moz-txt-link-freetext" href="https://cafnrfaculty.missouri.edu/tannerlab/">https://cafnrfaculty.missouri.edu/tannerlab/</a>
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A
From: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
<a class="moz-txt-link-rfc2396E" href="mailto:phenixbb-bounces@phenix-online.org"><phenixbb-bounces@phenix-online.org></a> on behalf of Viney Singh
<a class="moz-txt-link-rfc2396E" href="mailto:vineysingh22@gmail.com"><vineysingh22@gmail.com></a>
Date: Wednesday, January 12, 2022 at 6:52 AM
To: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a> <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
Subject: [phenixbb] regarding number of unique reflections
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.
Dear all,
First of all sorry for the novice question.
I processed one of my datasets using xds. Since I was not expecting
an anomalous signal, I kept Friedel's Law = True.
The number of unique reflections I got: 17,000
I used xds_ASCII.HKL after correct.LP and converted it to mtz using
Phenix with 10% reflections for Rfree calculations.
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.
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.
I would really appreciate if someone can guide me to resolve this
discrepancy.
Thanks in advance.
Viney
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Message: 4
Date: Wed, 12 Jan 2022 21:28:37 +0530
From: Viney Singh <a class="moz-txt-link-rfc2396E" href="mailto:vineysingh22@gmail.com"><vineysingh22@gmail.com></a>
To: "Tanner, John J." <a class="moz-txt-link-rfc2396E" href="mailto:TannerJJ@missouri.edu"><TannerJJ@missouri.edu></a>
Cc: <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org">"phenixbb@phenix-online.org"</a> <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
Subject: Re: [phenixbb] regarding number of unique reflections
Message-ID:
????<a class="moz-txt-link-rfc2396E" href="mailto:CALO_hTyJj3bSg_rev1hZVEvr=K91+C9x1AtbdrpiOajsSKk-Hg@mail.gmail.com"><CALO_hTyJj3bSg_rev1hZVEvr=K91+C9x1AtbdrpiOajsSKk-Hg@mail.gmail.com></a>
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Thanks a lot, Dr .Tanner. I will try the suggestion. Currently, I tried
running xds_ASCII.HKL on pointless followed by truncate. Seems like
mtz is
now all good. But I am wondering if this is the right way to go
about it?
On Wed, Jan 12, 2022 at 8:33 PM Tanner, John J. <a class="moz-txt-link-rfc2396E" href="mailto:TannerJJ@missouri.edu"><TannerJJ@missouri.edu></a>
wrote:
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">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.
--
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: <a class="moz-txt-link-abbreviated" href="mailto:tannerjj@missouri.edu">tannerjj@missouri.edu</a> <a class="moz-txt-link-rfc2396E" href="mailto:tannerjj@missouri.edu"><tannerjj@missouri.edu></a>
<a class="moz-txt-link-freetext" href="https://cafnrfaculty.missouri.edu/tannerlab/">https://cafnrfaculty.missouri.edu/tannerlab/</a>
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A
*From: *phenixbb-bounces@phenix-online.org <
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>> on behalf of Viney Singh <
<a class="moz-txt-link-abbreviated" href="mailto:vineysingh22@gmail.com">vineysingh22@gmail.com</a>>
*Date: *Wednesday, January 12, 2022 at 6:52 AM
*To: *phenixbb@phenix-online.org <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
*Subject: *[phenixbb] regarding number of unique reflections
*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.
Dear all,
First of all sorry for the novice question.
I *processed* one of my datasets using xds. Since I was not
expecting an
anomalous signal, I kept Friedel's Law = True.
The number of unique reflections I got: *17,000*
I used xds_ASCII.HKL after correct.LP and converted it to mtz using
Phenix
with 10% reflections for Rfree calculations.
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.
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*.
I would really appreciate if someone can guide me to resolve this
discrepancy.
Thanks in advance.
Viney
</pre>
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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>
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<p class="p1"><span class="s1">FRANCE</span></p>
<p class="p1"><span class="s1">+33 4 37 65 29 01</span></p>
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