The scripts and input files that accompany this demo can be found in the
demos/protocol_captures directory of the Rosetta weekly releases.
This is a protocol capture, and represents the protocol at a fixed point in time. It may not work with the current version of Rosetta.
KEYWORDS: MEMBRANES STRUCTURE_PREDICTION STABILITY_IMPROVEMENT
Follow the steps below. Example inputs and outputs are provided in the respective folders. Three different options are provided for variable flexibility:
cmd_mutate.sh only mutates and repacks the mutated residue cmd_mutate_repack.sh mutates and repacks within a radius of the mutation site cmd_mutate_relax.sh mutates and refines the entire protein with sidechain optimization.
1) Adjust the paths for the Rosetta executable and database in the cmd_mutate<...>.sh scripts. Make sure you understand the options in the cmd files.
While mutate and mutate_repack only require a single output model, mutate_relax requires more models. Choose a number between 50 and 1,000 for production runs, depending on the computational resources.
2) Run the scripts:
./cmd_mutate.sh ./cmd_mutate_repack.sh ./cmd_mutate_relax.sh
3) Check your output: the relevant output files have the desired mutation in the filename. Scores can be found in the PDBs after the ATOM lines.