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> > 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. > > R&D | Biologics Engineering > One Medimmune Way, Gaithersburg, MD 20878 > T: 301-398-5851 > vaheh.oganes...@astrazeneca.com > > > > From: John Berrisford <j...@ebi.ac.uk> > Sent: Monday, November 1, 2021 12:53 PM > To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com> > Cc: 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) 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 > > > > ------------------------- > > > > To unsubscribe from the CCP4BB list, click the following link: > > 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 ######################################################################## 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/
