The question was: "I am looking for a way to conserve side-chain conformations across mutate_replace. The default way muta_rep works is that it takes CHI1 and CHI2 angles from its database. However, if I have a molecular replacement solution and want to mutate the old structure's GLU to my structure's ASP, I would like O to take the CHI1 angle of my ASP from the previous GLU. Is there any way to do this ?"
You could keep a backup copy of your mol rep search model and try to use "merge_atoms" (don't know if it works if the residues are different, but assume it does); you probably need to do a "refi_zone" as well afterwards
Personally, I use the following 'protocol':
if the side chain dens is clear, then:
if the density is not clear: