Member Site › Forums › Rosetta 3 › Rosetta 3 – General › How to relax only one domain of a protein and keep the rest of them fixed › Reply To: How to relax only one domain of a protein and keep the rest of them fixed
No it doesn’t break the loops as I’ve added a chainbreak term to the score function with help from smlewis.
See attached script.
the arguments are:
python relax_loops.py reference.pdb pdb_to_relax.pdb start_resnum end_resnum
reference_pdb is just used to calculate RMSDs at the end but you can just put in the same file as for pdb_to_relax if you don’t have something to compare to. The resnums are internal Rosetta residue numbers not PDB residue numbers.
Let me know if this works. I’ve tried to reproduce what fast relax does.
It outputs to test_out.pdb but you can change this to something more user friendly.