I haven’t deposited any PDB entries for a while. The last time I did, I remember it not being completely trivial to add these loops. However, I was hoping that someone from wwPDB or CCP4 would weigh in with advice on how it can be done!
For those who use StarAniso, the current version makes a CIF file with the required loops, and they now have advice on their website about this: https://staraniso.globalphasing.org/deposition_about.html. Randy > On 18 Apr 2024, at 12:25, Frank von Delft <frank.vonde...@cmd.ox.ac.uk> wrote: > > Is it easy/non-arcane or indeed automatic for non-experts to add these loops? > Because that's the only way this will be achieved systemically. > > Presumably ccp4i2 can be wrangled into making it happen magically. (Apologies > if it does already, if so, a comment here would help the discussion...) > > Frank > > > > On 18/04/2024 11:02, Randy John Read wrote: >> I’d like to add my strong agreement to what Robbie said, but also point out >> a wrinkle. When the PDB runs validation, it just takes the data that are in >> the first reflection loop of the reflections.cif file. So if you want the >> validation statistics to match your reported refinement statistics, that >> loop should contain the set of data you gave the refinement program, >> especially if you’ve done something like apply an elliptical truncation, >> correct for anisotropy, or convert intensities to amplitudes, all of which >> change the data in ways that can’t be reversed later. Whenever you’ve done >> any of this (and many people are using StarAniso these days, which does all >> of those things), please put in a second reflection loop containing the >> whole set of intensities to the highest resolution you used, without any >> anisotropic scaling or elliptical cutoffs. Then anyone wanting to re-refine >> your structure or check your data for artefacts will have more information >> available. >> >> Of course, I hope we’re moving to a world in which we all also deposit the >> intensities before merging, which in principle allows even more quality >> control to be done. >> >> Best wishes, >> >> Randy Read >> >>> On 18 Apr 2024, at 05:04, Robbie Joosten <robbie_joos...@hotmail.com> wrote: >>> >>> If I may add to that: Please deposit the full dataset, not just the set of >>> reflections you end up using. This allows people to use all the data if >>> they are interested. >>> >>> Cheers, >>> Robbie >>> >>> On 17 Apr 2024 22:35, "Hekstra, Doeke Romke" <doeke_heks...@harvard.edu> >>> wrote: >>> Hi Matt, >>> I appreciate disagreement and comments from colleagues. My two cents are >>> that it seems unnecessary to repeat scaling and merging, or any earlier >>> step. If you want to remove structure factor amplitudes or merged >>> intensities from the MTZ file you can do so using MTZUTILS or similar >>> functionality in CCP4 >>> (https://www.ccp4.ac.uk/html/mtzutils.html#generalresolution). For >>> refinement, you can specify the desired resolution range in your favorite >>> refinement program. >>> My personal convention is to use CC1/2 = 0.30 as the point to which retain >>> data and <I/sigI> = 2 as the nominal resolution of the dataset. If you have >>> the HKL2000 scaling log, you should be able to retrieve this information. I >>> frankly wish we’d just deposit all data in the PDB rather than truncate >>> based on some criterion or another. >>> Best, Doeke >>> From: Matt Mcleod <mjmcleo...@gmail.com> >>> Sent: Wednesday, April 17, 2024 4:12 PM >>> To: Hekstra, Doeke Romke <doeke_heks...@harvard.edu> >>> Cc: CCP4BB@JISCMAIL.AC.UK >>> Subject: Re: [ccp4bb] Rescale merged data? >>> Sure thing. >>> A former student left somewhere between 30-50 datasets but they scaled the >>> data to the detector corners (or maybe edge) in HKL2000. There are many of >>> the high-resolution bins with no reflections in them. He then went forward >>> and merged this data, presumably in HKL2000 again and did his model >>> building/refinement. We now need to re-refine the models against this >>> data for publication but we need a more suitable resolution cutoff for the >>> data. >>> Rather than go back and index/integrate all the data and then rescale the >>> data to a more appropriate place (then merge), I was wondering if there was >>> a way to take the merged reflections as either .sca or .mtz (from >>> scalepacktomtz output) and then rescale to a more appropriate resolution. >>> It doesn't seem like the student left unmerged data. >>> So, nothing fancy (aniostropy etc), there is just a lot of data that needs >>> to be adjusted and I am trying to avoid reprocessing all the frames again. >>> Matt >>> On Wed, 17 Apr 2024 at 15:59, Hekstra, Doeke Romke >>> <doeke_heks...@harvard.edu> wrote: >>> Hi Matt, >>> >>> It would be helpful if you could describe your case in more detail. Do you >>> want to change the resolution cutoff after scaling? Do you want to keep >>> more data? Fewer? Or do you mean something different such as truncation to >>> generate amplitudes, application of anisotropic resolution cutoffs, or >>> outlier rejection? Are you referring to data that were scaled in HKL2000? >>> >>> Best, Doeke >>> >>> -----Original Message----- >>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Matt McLeod >>> Sent: Wednesday, April 17, 2024 3:04 PM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] Rescale merged data? >>> >>> Hi all, >>> >>> I am looking at a old students data and it looks like they didn't properly >>> cut off the data during scaling. All of the files I have appear to be the >>> merged .sca (or mtz after converting with scalepacktomtz) - is there a way >>> to retruncate the data after merging or do I have to reprocess the data? >>> >>> Thanks, >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a >>> mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are >>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> >>> -- >>> Matthew Jordan McLeod, PhD >>> Post-Doctoral Fellow - Cornell University >>> >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> On 17 Apr 2024 22:35, "Hekstra, Doeke Romke" <doeke_heks...@harvard.edu> >>> wrote: >>> Hi Matt, >>> I appreciate disagreement and comments from colleagues. My two cents are >>> that it seems unnecessary to repeat scaling and merging, or any earlier >>> step. If you want to remove structure factor amplitudes or merged >>> intensities from the MTZ file you can do so using MTZUTILS or similar >>> functionality in CCP4 >>> (https://www.ccp4.ac.uk/html/mtzutils.html#generalresolution). For >>> refinement, you can specify the desired resolution range in your favorite >>> refinement program. >>> My personal convention is to use CC1/2 = 0.30 as the point to which retain >>> data and <I/sigI> = 2 as the nominal resolution of the dataset. If you have >>> the HKL2000 scaling log, you should be able to retrieve this information. I >>> frankly wish we’d just deposit all data in the PDB rather than truncate >>> based on some criterion or another. >>> Best, Doeke >>> From: Matt Mcleod <mjmcleo...@gmail.com> >>> Sent: Wednesday, April 17, 2024 4:12 PM >>> To: Hekstra, Doeke Romke <doeke_heks...@harvard.edu> >>> Cc: CCP4BB@JISCMAIL.AC.UK >>> Subject: Re: [ccp4bb] Rescale merged data? >>> Sure thing. >>> A former student left somewhere between 30-50 datasets but they scaled the >>> data to the detector corners (or maybe edge) in HKL2000. There are many of >>> the high-resolution bins with no reflections in them. He then went forward >>> and merged this data, presumably in HKL2000 again and did his model >>> building/refinement. We now need to re-refine the models against this >>> data for publication but we need a more suitable resolution cutoff for the >>> data. >>> Rather than go back and index/integrate all the data and then rescale the >>> data to a more appropriate place (then merge), I was wondering if there was >>> a way to take the merged reflections as either .sca or .mtz (from >>> scalepacktomtz output) and then rescale to a more appropriate resolution. >>> It doesn't seem like the student left unmerged data. >>> So, nothing fancy (aniostropy etc), there is just a lot of data that needs >>> to be adjusted and I am trying to avoid reprocessing all the frames again. >>> Matt >>> On Wed, 17 Apr 2024 at 15:59, Hekstra, Doeke Romke >>> <doeke_heks...@harvard.edu> wrote: >>> Hi Matt, >>> >>> It would be helpful if you could describe your case in more detail. Do you >>> want to change the resolution cutoff after scaling? Do you want to keep >>> more data? Fewer? Or do you mean something different such as truncation to >>> generate amplitudes, application of anisotropic resolution cutoffs, or >>> outlier rejection? Are you referring to data that were scaled in HKL2000? >>> >>> Best, Doeke >>> >>> -----Original Message----- >>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Matt McLeod >>> Sent: Wednesday, April 17, 2024 3:04 PM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] Rescale merged data? >>> >>> Hi all, >>> >>> I am looking at a old students data and it looks like they didn't properly >>> cut off the data during scaling. All of the files I have appear to be the >>> merged .sca (or mtz after converting with scalepacktomtz) - is there a way >>> to retruncate the data after merging or do I have to reprocess the data? >>> >>> Thanks, >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a >>> mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are >>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> >>> -- >>> Matthew Jordan McLeod, PhD >>> Post-Doctoral Fellow - Cornell University >>> >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> On 17 Apr 2024 22:35, "Hekstra, Doeke Romke" <doeke_heks...@harvard.edu> >>> wrote: >>> Hi Matt, >>> I appreciate disagreement and comments from colleagues. My two cents are >>> that it seems unnecessary to repeat scaling and merging, or any earlier >>> step. If you want to remove structure factor amplitudes or merged >>> intensities from the MTZ file you can do so using MTZUTILS or similar >>> functionality in CCP4 >>> (https://www.ccp4.ac.uk/html/mtzutils.html#generalresolution). For >>> refinement, you can specify the desired resolution range in your favorite >>> refinement program. >>> My personal convention is to use CC1/2 = 0.30 as the point to which retain >>> data and <I/sigI> = 2 as the nominal resolution of the dataset. If you have >>> the HKL2000 scaling log, you should be able to retrieve this information. I >>> frankly wish we’d just deposit all data in the PDB rather than truncate >>> based on some criterion or another. >>> Best, Doeke >>> From: Matt Mcleod <mjmcleo...@gmail.com> >>> Sent: Wednesday, April 17, 2024 4:12 PM >>> To: Hekstra, Doeke Romke <doeke_heks...@harvard.edu> >>> Cc: CCP4BB@JISCMAIL.AC.UK >>> Subject: Re: [ccp4bb] Rescale merged data? >>> Sure thing. >>> A former student left somewhere between 30-50 datasets but they scaled the >>> data to the detector corners (or maybe edge) in HKL2000. There are many of >>> the high-resolution bins with no reflections in them. He then went forward >>> and merged this data, presumably in HKL2000 again and did his model >>> building/refinement. We now need to re-refine the models against this >>> data for publication but we need a more suitable resolution cutoff for the >>> data. >>> Rather than go back and index/integrate all the data and then rescale the >>> data to a more appropriate place (then merge), I was wondering if there was >>> a way to take the merged reflections as either .sca or .mtz (from >>> scalepacktomtz output) and then rescale to a more appropriate resolution. >>> It doesn't seem like the student left unmerged data. >>> So, nothing fancy (aniostropy etc), there is just a lot of data that needs >>> to be adjusted and I am trying to avoid reprocessing all the frames again. >>> Matt >>> On Wed, 17 Apr 2024 at 15:59, Hekstra, Doeke Romke >>> <doeke_heks...@harvard.edu> wrote: >>> Hi Matt, >>> >>> It would be helpful if you could describe your case in more detail. Do you >>> want to change the resolution cutoff after scaling? Do you want to keep >>> more data? Fewer? Or do you mean something different such as truncation to >>> generate amplitudes, application of anisotropic resolution cutoffs, or >>> outlier rejection? Are you referring to data that were scaled in HKL2000? >>> >>> Best, Doeke >>> >>> -----Original Message----- >>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Matt McLeod >>> Sent: Wednesday, April 17, 2024 3:04 PM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] Rescale merged data? >>> >>> Hi all, >>> >>> I am looking at a old students data and it looks like they didn't properly >>> cut off the data during scaling. All of the files I have appear to be the >>> merged .sca (or mtz after converting with scalepacktomtz) - is there a way >>> to retruncate the data after merging or do I have to reprocess the data? >>> >>> Thanks, >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a >>> mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are >>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> >>> -- >>> Matthew Jordan McLeod, PhD >>> Post-Doctoral Fellow - Cornell University >>> >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> On 17 Apr 2024 22:35, "Hekstra, Doeke Romke" <doeke_heks...@harvard.edu> >>> wrote: >>> Hi Matt, >>> I appreciate disagreement and comments from colleagues. My two cents are >>> that it seems unnecessary to repeat scaling and merging, or any earlier >>> step. If you want to remove structure factor amplitudes or merged >>> intensities from the MTZ file you can do so using MTZUTILS or similar >>> functionality in CCP4 >>> (https://www.ccp4.ac.uk/html/mtzutils.html#generalresolution). For >>> refinement, you can specify the desired resolution range in your favorite >>> refinement program. >>> My personal convention is to use CC1/2 = 0.30 as the point to which retain >>> data and <I/sigI> = 2 as the nominal resolution of the dataset. If you have >>> the HKL2000 scaling log, you should be able to retrieve this information. I >>> frankly wish we’d just deposit all data in the PDB rather than truncate >>> based on some criterion or another. >>> Best, Doeke >>> From: Matt Mcleod <mjmcleo...@gmail.com> >>> Sent: Wednesday, April 17, 2024 4:12 PM >>> To: Hekstra, Doeke Romke <doeke_heks...@harvard.edu> >>> Cc: CCP4BB@JISCMAIL.AC.UK >>> Subject: Re: [ccp4bb] Rescale merged data? >>> Sure thing. >>> A former student left somewhere between 30-50 datasets but they scaled the >>> data to the detector corners (or maybe edge) in HKL2000. There are many of >>> the high-resolution bins with no reflections in them. He then went forward >>> and merged this data, presumably in HKL2000 again and did his model >>> building/refinement. We now need to re-refine the models against this >>> data for publication but we need a more suitable resolution cutoff for the >>> data. >>> Rather than go back and index/integrate all the data and then rescale the >>> data to a more appropriate place (then merge), I was wondering if there was >>> a way to take the merged reflections as either .sca or .mtz (from >>> scalepacktomtz output) and then rescale to a more appropriate resolution. >>> It doesn't seem like the student left unmerged data. >>> So, nothing fancy (aniostropy etc), there is just a lot of data that needs >>> to be adjusted and I am trying to avoid reprocessing all the frames again. >>> Matt >>> On Wed, 17 Apr 2024 at 15:59, Hekstra, Doeke Romke >>> <doeke_heks...@harvard.edu> wrote: >>> Hi Matt, >>> >>> It would be helpful if you could describe your case in more detail. Do you >>> want to change the resolution cutoff after scaling? Do you want to keep >>> more data? Fewer? Or do you mean something different such as truncation to >>> generate amplitudes, application of anisotropic resolution cutoffs, or >>> outlier rejection? Are you referring to data that were scaled in HKL2000? >>> >>> Best, Doeke >>> >>> -----Original Message----- >>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Matt McLeod >>> Sent: Wednesday, April 17, 2024 3:04 PM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] Rescale merged data? >>> >>> Hi all, >>> >>> I am looking at a old students data and it looks like they didn't properly >>> cut off the data during scaling. All of the files I have appear to be the >>> merged .sca (or mtz after converting with scalepacktomtz) - is there a way >>> to retruncate the data after merging or do I have to reprocess the data? >>> >>> Thanks, >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a >>> mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are >>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> >>> -- >>> Matthew Jordan McLeod, PhD >>> Post-Doctoral Fellow - Cornell University >>> >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> On 17 Apr 2024 22:35, "Hekstra, Doeke Romke" <doeke_heks...@harvard.edu> >>> wrote: >>> Hi Matt, >>> I appreciate disagreement and comments from colleagues. My two cents are >>> that it seems unnecessary to repeat scaling and merging, or any earlier >>> step. If you want to remove structure factor amplitudes or merged >>> intensities from the MTZ file you can do so using MTZUTILS or similar >>> functionality in CCP4 >>> (https://www.ccp4.ac.uk/html/mtzutils.html#generalresolution). For >>> refinement, you can specify the desired resolution range in your favorite >>> refinement program. >>> My personal convention is to use CC1/2 = 0.30 as the point to which retain >>> data and <I/sigI> = 2 as the nominal resolution of the dataset. If you have >>> the HKL2000 scaling log, you should be able to retrieve this information. I >>> frankly wish we’d just deposit all data in the PDB rather than truncate >>> based on some criterion or another. >>> Best, Doeke >>> From: Matt Mcleod <mjmcleo...@gmail.com> >>> Sent: Wednesday, April 17, 2024 4:12 PM >>> To: Hekstra, Doeke Romke <doeke_heks...@harvard.edu> >>> Cc: CCP4BB@JISCMAIL.AC.UK >>> Subject: Re: [ccp4bb] Rescale merged data? >>> Sure thing. >>> A former student left somewhere between 30-50 datasets but they scaled the >>> data to the detector corners (or maybe edge) in HKL2000. There are many of >>> the high-resolution bins with no reflections in them. He then went forward >>> and merged this data, presumably in HKL2000 again and did his model >>> building/refinement. We now need to re-refine the models against this >>> data for publication but we need a more suitable resolution cutoff for the >>> data. >>> Rather than go back and index/integrate all the data and then rescale the >>> data to a more appropriate place (then merge), I was wondering if there was >>> a way to take the merged reflections as either .sca or .mtz (from >>> scalepacktomtz output) and then rescale to a more appropriate resolution. >>> It doesn't seem like the student left unmerged data. >>> So, nothing fancy (aniostropy etc), there is just a lot of data that needs >>> to be adjusted and I am trying to avoid reprocessing all the frames again. >>> Matt >>> On Wed, 17 Apr 2024 at 15:59, Hekstra, Doeke Romke >>> <doeke_heks...@harvard.edu> wrote: >>> Hi Matt, >>> >>> It would be helpful if you could describe your case in more detail. Do you >>> want to change the resolution cutoff after scaling? Do you want to keep >>> more data? Fewer? Or do you mean something different such as truncation to >>> generate amplitudes, application of anisotropic resolution cutoffs, or >>> outlier rejection? Are you referring to data that were scaled in HKL2000? >>> >>> Best, Doeke >>> >>> -----Original Message----- >>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Matt McLeod >>> Sent: Wednesday, April 17, 2024 3:04 PM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] Rescale merged data? >>> >>> Hi all, >>> >>> I am looking at a old students data and it looks like they didn't properly >>> cut off the data during scaling. All of the files I have appear to be the >>> merged .sca (or mtz after converting with scalepacktomtz) - is there a way >>> to retruncate the data after merging or do I have to reprocess the data? >>> >>> Thanks, >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a >>> mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are >>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> >>> -- >>> Matthew Jordan McLeod, PhD >>> Post-Doctoral Fellow - Cornell University >>> >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> ----- >> Randy J. Read >> Department of Haematology, University of Cambridge >> Cambridge Institute for Medical Research Tel: +44 1223 336500 >> The Keith Peters Building >> Hills Road E-mail: >> rj...@cam.ac.uk >> Cambridge CB2 0XY, U.K. >> www-structmed.cimr.cam.ac.uk >> >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a >> mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ > ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
