Update on this. It seems that I was wrong, and time spent reading the manual and various tutorials on PDBx/mmCIF would have yielded dividends. Who would have thought that (we all know that people write manuals solely for their own benefit ;-))?
However, thanks to all who replied off-board to tell me that the chain ID in legacy PDB format in _atom_site.auth_asym_id in the mmCIF, and not in either of the two items I mentioned previously. best wishes and happy Solstice! Harry > On 9 Jun 2023, at 15:57, Harry Powell > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi folks > > I’ve noticed that for some structures, the PDB file seems to have the mmCIF > entry for the “_atom_site.label_asym_id” as the chain ID, and for other PDB > files it has the “_atom_site.label_entity_id”. > > e.g. for 4bpq, for ATOM 1 I see - > >> CIF: ATOM 1 N N . UNK A 1 1 ? 14.187 19.549 -8.010 1.00 0.00 ? 1 >> UNK A N 1 >> >> PDB: ATOM 1 N UNK A 1 14.187 19.549 -8.010 1.00 0.00 >> N >> > but for 6p9o for ATOM 1 I see - > >> CIF: ATOM 1 N N . ARG A 1 64 ? -0.538 27.658 131.675 1.00 39.97 ? 64 ARG 1 N >> 1 64 UNP P03300 643 R >> >> PDB: ATOM 1 N ARG 1 64 -0.538 27.658 131.675 1.00 39.97 >> N > > both have the corresponding loop items in the same order > > loop_ > _atom_site.group_PDB > _atom_site.id > _atom_site.type_symbol > _atom_site.label_atom_id > _atom_site.label_alt_id > _atom_site.label_comp_id > _atom_site.label_asym_id > _atom_site.label_entity_id > _atom_site.label_seq_id > > so it shouldn’t be that the items are in a different order (which I think is > allowed in STAR formats). > > Any ideas which one is right? Or are they both right? Or both wrong? Or am I > wrong about this, and have just mis-read the entries? (the refinement program > for 6p9o is given as both REFMAC and “PHENIX” in the CIF - presumably > phenix.refine, but I wouldn’t bet my house on it). > > Harry > > ######################################################################## > > 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/ ######################################################################## 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/
