Hi all, If I open (as far as I can tell) the mmCIF for any structure in the wwPDB that contains both defined amino acids and UNK in the same chain, then the UNK section is treated as covalently bonded to the flanking sequence. This appears to be a bug in the mmCIF generation itself, not in the viewing software (ChimeraX, in this case): if I look in 7kzn as a random example, I see:
loop_ _pdbx_validate_polymer_linkage.id _pdbx_validate_polymer_linkage.PDB_model_num _pdbx_validate_polymer_linkage.auth_atom_id_1 _pdbx_validate_polymer_linkage.auth_asym_id_1 _pdbx_validate_polymer_linkage.auth_comp_id_1 _pdbx_validate_polymer_linkage.auth_seq_id_1 _pdbx_validate_polymer_linkage.PDB_ins_code_1 _pdbx_validate_polymer_linkage.label_alt_id_1 _pdbx_validate_polymer_linkage.auth_atom_id_2 _pdbx_validate_polymer_linkage.auth_asym_id_2 _pdbx_validate_polymer_linkage.auth_comp_id_2 _pdbx_validate_polymer_linkage.auth_seq_id_2 _pdbx_validate_polymer_linkage.PDB_ins_code_2 _pdbx_validate_polymer_linkage.label_alt_id_2 _pdbx_validate_polymer_linkage.dist 1 1 C X UNK 345 ? ? N X UNK 348 ? ? 10.08 2 1 C X UNK 396 ? ? N X UNK 403 ? ? 28.65 3 1 C Y UNK 281 ? ? N Y UNK 284 ? ? 6.72 4 1 C Y UNK 387 ? ? N Y UNK 394 ? ? 22.26 5 1 C Y UNK 420 ? ? N Y UNK 424 ? ? 12.82 Considering that the coords themselves generally seem fine, I guess this is happening post deposition? Best regards, Tristan ######################################################################## 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/
