On Fri, 4 Dec 2020 at 19:16, Dale Tronrud <de...@daletronrud.com> wrote: > > Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" is > exactly the problem.
It's not about "creating meaning" but about consistent naming. For humans. > "chain names" ( or "entity identifiers" if I > recall the mmCIF terminology correctly) are simply database "indexes". No, entity is a somewhat different thing (multiple chains can point to the same entity). entity_id is specified in addition to label_asym_id and auth_asym_id. asym = "structural element in the asymmetric unit" (so-called chain). > The values of indices are meaningless in themselves, they are just > unique values that can be used to unambiguously identify a record. In > principle, you could just assign random ISO characters (I don't think > mmCIF allows unicode) and the mmCIF would be considered identical. And then you'd use this random string also in a publication when referring to the chain, and in the user interface? > You are trying to force meaning to the characters with an index, and > that puts multiple types of information in a single field. As Robbie > said already exists, if you want to encode connectivity into the data > base you have to add records that define that connectivity. That places > the connectivity information explicitly in the data models and allows > standard data base tools to track and validate. No one was proposing to replace connectivity with names. It was about naming that will be easier to work with for people. > learn the sequence you have to go to the mmCIF records that define the > connectivity between residues. It is entirely possible that "3" comes > before "1" because these indexes don't contain any information, other > than being unique within the chain. In mmCIF you have label_seq_id that must be both unique and sequential. So 3 is always the third residue wrt to the full sequence. ######################################################################## 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/
