Dear Jasmine, thank you for this explanation. It's the best explanation of this remediation I've read.
The use of IDs may confuse people, so I'd like to reiterate it and ask for clarification. Every residue in the mmCIF format has three (3) independent chain IDs assigned to it (and three sequence numbers, and three residue names). In your example: J 4 NAG 1 I NAG 1 A NAG 1310 n J - asym_id = _atom_site.label_asym_id I - pdb_asym_id = _atom_site.auth_asym_id (?!) A - auth_asym_id = n/a (correct me if I got it wrong, but I see that _atom_site.auth_asym_id corresponds to _pdbx_branch_scheme.pdb_asym_id and not to auth_asym_id as one could expect). How to call these chain IDs? When I write software documentation, I need to refer to chain IDs (and sequence numbers), but I can't find proper words to clearly tell which ID I'm referring to. I was using hard to read names such as auth_asym_id, but now I see that even this is ambiguous. BTW, when you write that wwPDB encourages depositors to use the wwPDB-assigned chain ID in publications, which of the two wwPDB-assigned chain IDs do you mean? Thank you, Marcin ######################################################################## 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/
