In a pose, how can I replace the rotamer of a particular residue? I know I can use the pose.replace_residue function to change the amino acid type at the residue at seqpos in the pose sequence.
replace_residue (Size const seqpos, Residue const &new_rsd_in, bool const orient_backbone)
Replaces the residue at with
replace_residue can also be used to change the rotamer. All you need to do is have a Residue object which contains whatever rotamer you want to replace it with. So the internally stored Residue object with the existing conformation will be replaced with the Rotamer object you supply which has your desired rotameric state. (Do you have that already, or how are you obtaining/representing the rotamer you want to use?)