I see that Coot exports to PDB with an invalid HETNAM field, putting 5-letter code in place of the 3 letter code. This is unnecessary and breaks the PDB format rules. I will give an example, along with my suggestion for the correct way to handle conversion.
First, the 3-letter residue name has never been a real limitation, only a limitation in the simplistic way software has been written. The HETNAM record was designed specifically to avoid global name collisions, by declaring a local short name linked to the global long name. Now that we are forced to abandon the simple 3-letter globals, simply declaring PDB format obsolete is unwarranted. Its simplicity for most uses will keep it alive for a very long time. Likewise, I think the complexity of CIF is aimed at databases, and not experimental structure determination. Consider structure 9NQP.cif, which the following data elements to define the ligand: pdbx_entity_nonpoly.comp_id = A1BXB entity.pdbx_description = Pritelivir chem_comp.pdbx_synonym = 'N-methyl-N-(4-methyl-5-sulfamoyl-1,3-thiazol-2-yl)-2-[4-(pyridin-2-yl)phenyl]acetamide' pdbx_nonpoly_scheme.auth_mon_id = PTL >From this we can easily asses that an actually useful working 3-letter code for use in the file-local scope should be what the author used (A useful new data field from CIF), the primary name, a synonym, and the comp_id global database key: I propose that the PDB format should be as follows, and is fully compatible with existing PDB format: HETNAM PTL Pritelivir HETSYN PTL N-methyl-N-(4-methyl-5-sulfamoyl-1,3-thiazol-2-yl)-2-[4-(pyridin- HETSYN 2 2-yl)phenyl]acetamide HETSYN PTL A1BXB or optionally tag the comp_id as: HETSYN PTL comp_id:A1BXB The original specs for HETNAM, HETSYN don't include any sort of label, and can easily be processed as "In the database of ligands, use the first lookup string that matches" but since structural biologists aren't running databases, we can avoid the slow-down of full database lookup by including the quick comp_id: name label. This is a simple solution to what really is not a format problem, but an implementation problem. The above method will work with all existing software, with the caveat that PTL will give an invalid assumption about a global comp_id, which would in most cases be handled as unknown ligands are already handled, and a very quick software update to actually use the HETNAM, HETSYN data. Juno Krahn ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
