Swapaa replaces every residue with at least one atom in atom-spec with a new_type residue. New_type is a three-letter residue name for one of the 20 standard amino acids, with the exception of HIS. Instead of HIS for histidine, it is necessary to indicate HID (neutral, protonated at ND), HIE (neutral, protonated at NE), or HIP (positively charged, protonated at both ND and NE). New_type can be in lowercase or capital letters. Residues swapped into models with hydrogens will include hydrogens, whereas residues swapped into models without hydrogens will not. (Note that hydrogens can be added with AddH.) The geometries of the new residues, especially proline, may not be optimal.
The temperature factor for the new residue is set to the highest currently found in the model.
The keyword preserve is recognized, but currently does not affect swapaa behavior in any way.