I am wondering if Rosetta has an app for detecting brakes and clashes in proteins? I have got an ensembles of protein decoys that were rebuilt from Ca and Cb traces, then idealized and relaxed. Some of the decoys have clashes, others have brakes. I would like to filter "bad" decoys out.
My other question is about the "bb_min_allowed_dev" option. Does it work with the Rosetta's relaxation? I am wondering whether or no increasing "bb_min_allowed_dev" to 0.7-1.0A would remove some severe clashes?