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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. MSE residues are 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 IOData.hetatm is False, it will still be read in). This behavior can be disabled by setting this variable to False.