io_data.convert_modres — whether to convert modified residues

By default, 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. In all cases, these residues are then treated as regular amino acids ('ATOM' records) regardless of whether they are marked as 'ATOM' or 'HETATM' in the PDB or mmCIF file (thus, even if the modified residue is marked as 'HETATM' and io_data.hetatm is False, it will still be read in). This behavior can be disabled by setting this variable to False.