[phenixbb] refinement of an ensemble of structures -> cryoEM variability
Oliver Clarke
olibclarke at gmail.com
Thu Jan 13 09:53:20 PST 2022
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 <jmholton at lbl.gov>
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] refinement of an ensemble of structures ->
> cryoEM variability
> Message-ID: <92b5f0e3-c4b1-59f9-1c38-50fffcda0bb1 at lbl.gov>
> 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 <vincent.chaptal at ibcp.fr>
>>> To: Guillaume Gaullier <guillaume.gaullier at icm.uu.se>, Pavel Afonine
>>> <pafonine at lbl.gov>
>>> Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
>>> Subject: Re: [phenixbb] refinement of an ensemble of structures ->
>>> cryoEM variability
>>> Message-ID: <ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3 at ibcp.fr>
>>> 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 <pafonine at lbl.gov> 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
>>>>>>
>>>>>> phenixbb at phenix-online.org
>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>>>
>>>>>> Unsubscribe:
>>>>>> phenixbb-leave at phenix-online.org
>>>>> _______________________________________________
>>>>> phenixbb mailing list
>>>>> phenixbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>> 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/
>>>
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
>>> URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20220112/e891a7ad/attachment-0001.htm>
>>>
>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Wed, 12 Jan 2022 18:11:02 +0530
>>> From: Viney Singh <vineysingh22 at gmail.com>
>>> To: phenixbb at phenix-online.org
>>> Subject: [phenixbb] regarding number of unique reflections
>>> Message-ID:
>>> <CALO_hTx1dtmm2nfkd4+9iPUb+jmAq4kM2ObB=jwrQ5VvCuUTmQ at 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 --------------
>>> An HTML attachment was scrubbed...
>>> 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." <TannerJJ at missouri.edu>
>>> To: Viney Singh <vineysingh22 at gmail.com>, "phenixbb at phenix-online.org"
>>> <phenixbb at phenix-online.org>
>>> Subject: Re: [phenixbb] regarding number of unique reflections
>>> Message-ID:
>>> <CH0PR01MB7154E88CABD14AE39C4FD543A7529 at 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: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>
>>> https://cafnrfaculty.missouri.edu/tannerlab/
>>> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
>>> Office: Schlundt Annex 203A
>>>
>>>
>>>
>>>
>>> From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Viney Singh <vineysingh22 at gmail.com>
>>> Date: Wednesday, January 12, 2022 at 6:52 AM
>>> To: phenixbb at phenix-online.org <phenixbb at phenix-online.org>
>>> 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 <vineysingh22 at gmail.com>
>>> To: "Tanner, John J." <TannerJJ at missouri.edu>
>>> Cc: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
>>> Subject: Re: [phenixbb] regarding number of unique reflections
>>> Message-ID:
>>> <CALO_hTyJj3bSg_rev1hZVEvr=K91+C9x1AtbdrpiOajsSKk-Hg at 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. <TannerJJ at missouri.edu>
>>> 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: tannerjj at missouri.edu <tannerjj at missouri.edu>
>>>> https://cafnrfaculty.missouri.edu/tannerlab/
>>>>
>>>> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
>>>>
>>>> Office: Schlundt Annex 203A
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> *From: *phenixbb-bounces at phenix-online.org <
>>>> phenixbb-bounces at phenix-online.org> on behalf of Viney Singh <
>>>> vineysingh22 at gmail.com>
>>>> *Date: *Wednesday, January 12, 2022 at 6:52 AM
>>>> *To: *phenixbb at phenix-online.org <phenixbb at phenix-online.org>
>>>> *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/20220112/094a7f44/attachment.htm>
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>> End of phenixbb Digest, Vol 194, Issue 2
>>> ****************************************
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 13 Jan 2022 09:42:52 -0800
> From: Pavel Afonine <pafonine at lbl.gov>
> To: James Holton <jmholton at lbl.gov>, phenixbb at phenix-online.org
> Subject: Re: [phenixbb] refinement of an ensemble of structures ->
> cryoEM variability
> Message-ID: <77affc31-47d5-c84d-a788-36d790c2d70b at lbl.gov>
> 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 <vincent.chaptal at ibcp.fr>
>>>> To: Guillaume Gaullier <guillaume.gaullier at icm.uu.se>,??? Pavel Afonine
>>>> ????<pafonine at lbl.gov>
>>>> Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
>>>> Subject: Re: [phenixbb] refinement of an ensemble of structures ->
>>>> ????cryoEM variability
>>>> Message-ID: <ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3 at ibcp.fr>
>>>> 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 <pafonine at lbl.gov> 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
>>>>>>>
>>>>>>> phenixbb at phenix-online.org
>>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>>>>
>>>>>>> Unsubscribe:
>>>>>>> phenixbb-leave at phenix-online.org
>>>>>> _______________________________________________
>>>>>> phenixbb mailing list
>>>>>> phenixbb at phenix-online.org
>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>>> 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/
>>>>
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>> URL:
>>>> <http://phenix-online.org/pipermail/phenixbb/attachments/20220112/e891a7ad/attachment-0001.htm>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 2
>>>> Date: Wed, 12 Jan 2022 18:11:02 +0530
>>>> From: Viney Singh <vineysingh22 at gmail.com>
>>>> To: phenixbb at phenix-online.org
>>>> Subject: [phenixbb] regarding number of unique reflections
>>>> Message-ID:
>>>> ????<CALO_hTx1dtmm2nfkd4+9iPUb+jmAq4kM2ObB=jwrQ5VvCuUTmQ at 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 --------------
>>>> An HTML attachment was scrubbed...
>>>> 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." <TannerJJ at missouri.edu>
>>>> To: Viney Singh <vineysingh22 at gmail.com>, "phenixbb at phenix-online.org"
>>>> ????<phenixbb at phenix-online.org>
>>>> Subject: Re: [phenixbb] regarding number of unique reflections
>>>> Message-ID:
>>>> ????<CH0PR01MB7154E88CABD14AE39C4FD543A7529 at 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: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>
>>>> https://cafnrfaculty.missouri.edu/tannerlab/
>>>> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
>>>> Office: Schlundt Annex 203A
>>>>
>>>>
>>>>
>>>>
>>>> From: phenixbb-bounces at phenix-online.org
>>>> <phenixbb-bounces at phenix-online.org> on behalf of Viney Singh
>>>> <vineysingh22 at gmail.com>
>>>> Date: Wednesday, January 12, 2022 at 6:52 AM
>>>> To: phenixbb at phenix-online.org <phenixbb at phenix-online.org>
>>>> 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 <vineysingh22 at gmail.com>
>>>> To: "Tanner, John J." <TannerJJ at missouri.edu>
>>>> Cc: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
>>>> Subject: Re: [phenixbb] regarding number of unique reflections
>>>> Message-ID:
>>>> ????<CALO_hTyJj3bSg_rev1hZVEvr=K91+C9x1AtbdrpiOajsSKk-Hg at 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. <TannerJJ at missouri.edu>
>>>> 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: tannerjj at missouri.edu <tannerjj at missouri.edu>
>>>>> https://cafnrfaculty.missouri.edu/tannerlab/
>>>>>
>>>>> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
>>>>>
>>>>> Office: Schlundt Annex 203A
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> *From: *phenixbb-bounces at phenix-online.org <
>>>>> phenixbb-bounces at phenix-online.org> on behalf of Viney Singh <
>>>>> vineysingh22 at gmail.com>
>>>>> *Date: *Wednesday, January 12, 2022 at 6:52 AM
>>>>> *To: *phenixbb at phenix-online.org <phenixbb at phenix-online.org>
>>>>> *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/20220112/094a7f44/attachment.htm>
>>>>
>>>> ------------------------------
>>>>
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>>
>>>> End of phenixbb Digest, Vol 194, Issue 2
>>>> ****************************************
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>
>
> ------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
> End of phenixbb Digest, Vol 194, Issue 4
> ****************************************
More information about the phenixbb
mailing list