On Sat, Feb 13, 2021, Nicholas Larsen wrote:
I hope this doesn't confuse the discussion, but my understanding was "UNK" stood for "unknown" residue and this will cause errors.
UNK is a legitimate entry in the components.cif collection. It's name is indeed "UNKNOWN", but it is of type "L-PEPTIDE LINKING", and has a peptide bond and CB and CG atoms (only) on the side chain, which doesn't correspond to any common amino acid. For this reason, it is a difficult residue to deal with for programs that expect to model real chemistry. Many entries never have a CG atom in a UNK residue, so an internal workaround we use is to convert to ALA, trying to remember to convert back to UNK for any output files that would be shared with others. Many PDB-like files in the wild use "UNK" for anything that is unknown, such as a ligand. One can hope that such usage will decline as standard-conformance becomes more widespread. ....dave case ######################################################################## 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/
