I am dealing with a PDB file missing some residues. I think I should clean it by clean_pdb.py of Rosetta or cleanATOM of PyRosetta.
In Rosetta, the clean_pdb ignores the missing positions and renumber all the residues from 1 to the end regardless of the missing gap.
In PyRosetta, the missing gap can still be remained.
Can I ask can I get the result similar to cleanATOM by using Rosetta's clean_pdb.py? I think I should clean the PDB first, then do loop modeling for the missing residues. Is that correct?
Thank you very much.