Hello everyone, recently I've been trying to make a homology model with a protein chain along with a nucleotide chain within it based on an existing template, but .
post-partial threading Rosetta dislocates the nucleotides nearly 1000 angstrom away from the structure. .
In principal, I'm suspecting this to be a result of an unwanted interaction between the nucleotide parameters and the protein which makes me wonder if their is a way to make cm_rosetta treat a specific chain/s as a rigid body ? In a sense, like I would with a ligand ?
My flags are these :
Thanks in advance to all the helpers !