Dear John Helliwell, I should have been more clear in addressing my email. It was in response to John Berrisford’s answer.
Regards, Vaheh From: John R Helliwell <jrhelliw...@gmail.com> Sent: Monday, November 1, 2021 3:13 PM To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com> Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] renaming chains Dear Valeh Apologies, I was solely replying to the numbering/labelling of waters observation/query of Mohamed, ie as a function of in situ parameter (time, temperature and pressure). Best wishes John Emeritus Professor John R Helliwell DSc On 1 Nov 2021, at 18:39, Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com>> wrote: Hi John, Thank you for explanation. The most recent encounter I had on this issue was with 3DMM and 3B9K. You would know better what caused chain renaming here, but it doesn’t look like any of the two scenarios you describe. Whatever the reason was I’m glad to hear that this is not a widespread rule that applies to all structures. Regards, Vaheh Oganesyan, Ph.D. [cid:image001.png@01D7CF33.8D9C2020] R&D | Biologics Engineering One Medimmune Way, Gaithersburg, MD 20878 T: 301-398-5851 vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com> From: John Berrisford <j...@ebi.ac.uk<mailto:j...@ebi.ac.uk>> Sent: Monday, November 1, 2021 12:53 PM To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com>> Cc: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk> Subject: Re: [ccp4bb] renaming chains Dear Vaheh Usually we do not rename chains as part of the curation procedure. There are instances when we do, for example when a chain has to be split into two chains and a new chain has to be defined, but this isn't typical. Because of this the wwPDB mmCIF file for each entry will usually contain the chains as defined by the depositor. If two letter chain IDs were used by the depositor then this is incompatible with the PDB format and a best effort PDB file is created. This will contain remapped chain IDs with a single letter for the chains. If you are using this best effort PDB file then I would encourage using the mmCIF file instead. If this is not the case, please can you share examples through our helpdesk (deposit-h...@mail.wwpdb.org<mailto:deposit-h...@mail.wwpdb.org>) where this has occurred so we can investigate. Many thanks John On 2021-11-01 15:00, Oganesyan, Vaheh wrote: > Hi All, > > This question is mostly for RCSB and PDBe: why are you renaming chains > in the deposited PDB files? Why does it matter what letter is assigned > to the chain? For 1,2 or 3 chain structures it is manageable, but for > more chains and/or many complexes per asu this becomes quite a > challenge. And if chains are similar in shape it is a real pain. > Reading associated manuscripts and looking at those structures is an > additive that feels unnecessary. > > Thank you in advance for explaining the logic behind. > > Vaheh Oganesyan, Ph.D. > > R&D | Biologics Engineering > > One Medimmune Way, Gaithersburg, MD 20878 > > T: 301-398-5851 > > vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com> > > ------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<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 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/
