"/Some special handling is done for certain commonly-used modified
residues. The MSE residue type is mapped to the regular MET amino
acid, and the SE atom in this residue is mapped to SD. The MEX and
ABU residue types are both mapped to CYS./"
...
I recently encountered PDB ID 3OW6. This structure includes a ligand
labeled MEX. The ligand does not resemble CYS, and the presence of MEX
causes an error. I'm reluctant to set io_data.convert_modres to False,
because I'd like to handle other modified residues (ex. MSE).
This part of the Modeller code is ancient, at least 15 years old, and
PDB has changed a lot since then. I don't see any examples of MEX used
as a polymer in current PDB (and only 1 example of it used as a ligand,
in 3ow6 as you noted) and only 3 examples of ABU polymer. Since neither
MEX nor ABU look much like CYS, I will remove this code entirely from
the next Modeller release - they can't be considered "commonly-used
modified residues" and it is probably causing more harm than good. (Of
course, if anybody relies on this ABU/MEX->CYS mapping, 1. it is easy to
work around and 2. let me know!)