When I were preparing some PDB files of crystal structures for Rosetta simulation, there are several ways to go after I checked Rosetta manuals and demos.
First method is following the doc 'Documentation for relax pdb with all-atom constraints / prepare pdb for rosetta with relax' in user guide and the codes in demos/prepare_pdb_for_rosetta_with_relax/. Breifly, it is using "relax" with some extra options e.g. '-relax:constrain_relax_to_start_coords'.
Another method is mentioned in doc 'Documentation for ddg_monomer application' where a helper application 'minimize_with_cst' is used.
I have no idea what is the difference between the two approaches and which one is more preferable in practical applications. So anyone can give some details about the backends?
Personally I prefer 'minimize_with_cst' because it can keep the original chain IDs in PDB, while 'relax' always renumbers the chain IDs to 'A B C D ...' even the option "-out:file:renumber_pdb false" is used.
Is there any way to let 'relax' not to renumber chain IDs?