Re: [ccp4bb] Data reprocessing
I have one or two in my garage ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 27 Jan 2024, 19:46, Randy John Read wrote: > Hi, The current policy of the PDB is that you can deposit a re-refinement of > a structure deposited by someone else only if you publish a new paper about > it, so that there is a citation associated with the structure. Of course, > echoing Eleanor, if you find an issue with someone else’s structure the most > collegiate thing to do is to inform the authors and attempt to work with them > to fix up the problem. Best wishes, Randy > On 27 Jan 2024, at 07:00, Eleanor > Dodson wrote: > > Did you make the original deposition ? If so the pdb > accepts re-depositions... > > If it was done by someone else I guess the > courteous thing is to notify them and maybe talk to the pdb- redo team? > > Cheers Eleanor > > On Sat, 27 Jan 2024 at 01:53, Lucas Souza wrote: > Dear > all, > > After auditing and reprocessing a deposited structure with clear > processing mistakes (missing/wrong residues and ligands with evident density) > prior to some analysis that are going to be published, what should be done? > Re-deposit the structure with a "reprocess" flag? Reopen the PDB deposition > and update the files? Or simply state in the publication that the data was > reprocessed? > > I'm curious if there's a consensus on handling situations of > this nature. > > Cheers, > Lucas > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > > To unsubscribe from the > CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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=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/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Data reprocessing
Hi, The current policy of the PDB is that you can deposit a re-refinement of a structure deposited by someone else only if you publish a new paper about it, so that there is a citation associated with the structure. Of course, echoing Eleanor, if you find an issue with someone else’s structure the most collegiate thing to do is to inform the authors and attempt to work with them to fix up the problem. Best wishes, Randy > On 27 Jan 2024, at 07:00, Eleanor Dodson > <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > Did you make the original deposition ? If so the pdb accepts re-depositions... > > If it was done by someone else I guess the courteous thing is to notify them > and maybe talk to the pdb- redo team? > Cheers Eleanor > > On Sat, 27 Jan 2024 at 01:53, Lucas Souza > wrote: > Dear all, > > After auditing and reprocessing a deposited structure with clear processing > mistakes (missing/wrong residues and ligands with evident density) prior to > some analysis that are going to be published, what should be done? Re-deposit > the structure with a "reprocess" flag? Reopen the PDB deposition and update > the files? Or simply state in the publication that the data was reprocessed? > > I'm curious if there's a consensus on handling situations of this nature. > > Cheers, > Lucas > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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=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/
Re: [ccp4bb] Data reprocessing
I second Eleanor's suggestions. In fact I would hope the PDB made re-depisitions known to the original authors. I had an incident recently where someone (I believe possibly a student) had used one of my structures for MR but then did the deposition as a re-refinement (because they used it as MR for their structure and were confused). Structure was not published so no reviewers saw it but still had a flag of being re-refined on my structure for quite a while before I noticed it unfortunately On Sat, 27 Jan 2024, 07:01 Eleanor Dodson, < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > Did you make the original deposition ? If so the pdb accepts > re-depositions... > > If it was done by someone else I guess the courteous thing is to notify > them and maybe talk to the pdb- redo team? > Cheers Eleanor > > On Sat, 27 Jan 2024 at 01:53, Lucas Souza > wrote: > >> Dear all, >> >> After auditing and reprocessing a deposited structure with clear >> processing mistakes (missing/wrong residues and ligands with evident >> density) prior to some analysis that are going to be published, what should >> be done? Re-deposit the structure with a "reprocess" flag? Reopen the PDB >> deposition and update the files? Or simply state in the publication that >> the data was reprocessed? >> >> I'm curious if there's a consensus on handling situations of this nature. >> >> Cheers, >> Lucas >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Data reprocessing
Did you make the original deposition ? If so the pdb accepts re-depositions... If it was done by someone else I guess the courteous thing is to notify them and maybe talk to the pdb- redo team? Cheers Eleanor On Sat, 27 Jan 2024 at 01:53, Lucas Souza wrote: > Dear all, > > After auditing and reprocessing a deposited structure with clear > processing mistakes (missing/wrong residues and ligands with evident > density) prior to some analysis that are going to be published, what should > be done? Re-deposit the structure with a "reprocess" flag? Reopen the PDB > deposition and update the files? Or simply state in the publication that > the data was reprocessed? > > I'm curious if there's a consensus on handling situations of this nature. > > Cheers, > Lucas > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
