I am working on a script that takes a given cleaned (using the cleaning.py script) pdb file (attached as dG_calc.txt) that mutates each residue through the sequence of amino acids and calculates the dG and ddG. This is based on the ala_scan.py script except no docking or other things.
I had a couple of questions:
1) Does the mutate_residue in PyRosetta 2.0 repack the side chains automatically? If so to what distance?
2) If not, does PackRotamersMover take care of this? If I need to use this I should restrict the packer so it only uses the original amino acids?
3) Before I start mutating the PDB structure should I minimize it using PackRotamersMover and then rescore it? Or is there another way to minimize the structure? I read on the forum here that pdb should be minimized first before being used in PyRosetta
Thanks for your input and help.