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
Date: Thu, 13 Jan 2022 09:26:50 -0800
From: James Holton <[email protected]>
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:
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

Message: 1
Date: Wed, 12 Jan 2022 10:36:27 +0100
From: vincent Chaptal <[email protected]>
To: Guillaume Gaullier <[email protected]>,	Pavel Afonine
	<[email protected]>
Cc: PHENIX user mailing list <[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"

Hi Guillaume,

thanks for the backup.
It's exactly my feeling also.

Best
Vincent

Le 12/01/2022 ? 10:09, Guillaume Gaullier a ?crit?:
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 https://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


On 11 Jan 2022, at 17:16, Pavel Afonine <[email protected]> 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

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N?r du har kontakt med oss p? Uppsala universitet med e-post s?
inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om
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E-mailing Uppsala University means that we will process your personal
data. For more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
-- 

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/

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Message: 2
Date: Wed, 12 Jan 2022 18:11:02 +0530
From: Viney Singh <[email protected]>
To: [email protected]
Subject: [phenixbb] regarding number of unique reflections
Message-ID:
	<CALO_hTx1dtmm2nfkd4+9iPUb+jmAq4kM2ObB=jwrQ5VvCuUTmQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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." <[email protected]>
To: Viney Singh <[email protected]>, "[email protected]"
	<[email protected]>
Subject: Re: [phenixbb] regarding number of unique reflections
Message-ID:
	<CH0PR01MB7154E88CABD14AE39C4FD543A7529@CH0PR01MB7154.prod.exchangelabs.com>
	
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: [email protected]<mailto:[email protected]>
https://cafnrfaculty.missouri.edu/tannerlab/
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A




From: [email protected] <[email protected]> on behalf of Viney Singh <[email protected]>
Date: Wednesday, January 12, 2022 at 6:52 AM
To: [email protected] <[email protected]>
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 <[email protected]>
To: "Tanner, John J." <[email protected]>
Cc: "[email protected]" <[email protected]>
Subject: Re: [phenixbb] regarding number of unique reflections
Message-ID:
	<CALO_hTyJj3bSg_rev1hZVEvr=K91+C9x1AtbdrpiOajsSKk-Hg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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. <[email protected]>
wrote:

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: [email protected] <[email protected]>
https://cafnrfaculty.missouri.edu/tannerlab/

Lab: Schlundt Annex rooms 3,6,9, 203B, 203C

Office: Schlundt Annex 203A









*From: *[email protected] <
[email protected]> on behalf of Viney Singh <
[email protected]>
*Date: *Wednesday, January 12, 2022 at 6:52 AM
*To: *[email protected] <[email protected]>
*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: Thu, 13 Jan 2022 09:42:52 -0800
From: Pavel Afonine <[email protected]>
To: James Holton <[email protected]>, [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?
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


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

Message: 1
Date: Wed, 12 Jan 2022 10:36:27 +0100
From: vincent Chaptal <[email protected]>
To: Guillaume Gaullier <[email protected]>,??? Pavel Afonine
????<[email protected]>
Cc: PHENIX user mailing list <[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"

Hi Guillaume,

thanks for the backup.
It's exactly my feeling also.

Best
Vincent

Le 12/01/2022 ? 10:09, Guillaume Gaullier a ?crit?:
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 https://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


On 11 Jan 2022, at 17:16, Pavel Afonine <[email protected]> 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:
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_______________________________________________
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[email protected]
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Unsubscribe: [email protected]
Page Title







N?r du har kontakt med oss p? Uppsala universitet med e-post s?
inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om
hur vi g?r det kan du l?sa h?r:
http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal
data. For more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
-- 

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/

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------------------------------

Message: 2
Date: Wed, 12 Jan 2022 18:11:02 +0530
From: Viney Singh <[email protected]>
To: [email protected]
Subject: [phenixbb] regarding number of unique reflections
Message-ID:
????<CALO_hTx1dtmm2nfkd4+9iPUb+jmAq4kM2ObB=jwrQ5VvCuUTmQ@mail.gmail.com> 

Content-Type: text/plain; charset="utf-8"

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
-------------- next part --------------
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URL: 
<http://phenix-online.org/pipermail/phenixbb/attachments/20220112/f1d16873/attachment-0001.htm>

------------------------------

Message: 3
Date: Wed, 12 Jan 2022 15:03:49 +0000
From: "Tanner, John J." <[email protected]>
To: Viney Singh <[email protected]>, "[email protected]"
????<[email protected]>
Subject: Re: [phenixbb] regarding number of unique reflections
Message-ID:
????<CH0PR01MB7154E88CABD14AE39C4FD543A7529@CH0PR01MB7154.prod.exchangelabs.com> 


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: [email protected]<mailto:[email protected]>
https://cafnrfaculty.missouri.edu/tannerlab/
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A




From: [email protected] 
<[email protected]> on behalf of Viney Singh 
<[email protected]>
Date: Wednesday, January 12, 2022 at 6:52 AM
To: [email protected] <[email protected]>
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: 
<http://phenix-online.org/pipermail/phenixbb/attachments/20220112/70d938d1/attachment-0001.htm>

------------------------------

Message: 4
Date: Wed, 12 Jan 2022 21:28:37 +0530
From: Viney Singh <[email protected]>
To: "Tanner, John J." <[email protected]>
Cc: "[email protected]" <[email protected]>
Subject: Re: [phenixbb] regarding number of unique reflections
Message-ID:
????<CALO_hTyJj3bSg_rev1hZVEvr=K91+C9x1AtbdrpiOajsSKk-Hg@mail.gmail.com> 

Content-Type: text/plain; charset="utf-8"

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. <[email protected]>
wrote:

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: [email protected] <[email protected]>
https://cafnrfaculty.missouri.edu/tannerlab/

Lab: Schlundt Annex rooms 3,6,9, 203B, 203C

Office: Schlundt Annex 203A









*From: *[email protected] <
[email protected]> on behalf of Viney Singh <
[email protected]>
*Date: *Wednesday, January 12, 2022 at 6:52 AM
*To: *[email protected] <[email protected]>
*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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--

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/