Hi Bernhard, > Coot, better mmdb, picks up _atom_site.auth_seq_id in the first instance > as residue number. So, here we have 17 twice. > Of course we have an > insertion code but in the "strict" setting of Coot we do not allow this > at the moment and warn of duplicated residues (see FAQ). I am not sure > if this has ever been an issue with cif files, certainly for pdb files > therefore the pedantry at the moment.
Just to clarify: it's sequence id (sequence number + insertion code) that must be unique. The residue sequence number can be duplicated (that's the point of having insertion codes) and coot/mmdb only check for uniqueness of sequence id. The problem here is that mmdb apparently doesn't read pdbx_PDB_ins_code as an insertion code. This is actually confusing in PDBx/mmCIF files. The auth_seq_id field, according to its name and description, should be the sequence id (i.e. it should include insertion code). And that's what it was in older mmCIF files. Currently in all the wwPDB files auth_seq_id is only the sequence number, and the insertion code is in separate field called pdbx_PDB_ins_code. To make it even more confusing, pdbx_PDB_ins_code is written next to label_seq_id (although it has nothing to do with label_seq_id) and seven columns away from auth_seq_id which it should be part of. Marcin ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
