I have a protein topology with a strange backbone (attached).
You can see that there is structure (several helices), but the backbone itself is not good enough to be able to do anything computationally with it, if ported into PyRosetta, PyRosetta it gets confused. So my question is how can I fix this backbone, nothing fancy just replace each position with Glycine or Valine or Alenine, but the proper ideal structure of the amino acid that will not result in clashed nor atoms occupying the same space?
I tried relaxing the structure, but that denatured that whole topology and did not fix the backbone.
I tried mutating each residue, but that only replaced the side chain and did now add a new residue with the correct backbone
I tried pyrosetta.rosetta.protocols.forge.remodel.RemodelMover() but that ended up in an infinite loop (it ran for 24 hours without stopping), but I ran it "raw" without a blueprint file, so maybe it need some more spesifications?
Any advice how I can fix this backbone without making majore changes to the topology? I am not interested in the sidechain because I have other methods to deal with them, but the backbone.
My simple code:
from pyrosetta import * from pyrosetta.toolbox import * init() pose = pose_from_pdb('Backbone.pdb') mover = pyrosetta.rosetta.protocols.forge.remodel.RemodelMover() mover.apply(pose) pose.dump_pdb('test.pdb')