- The version of Rosetta underlying Cyrus Bench CAD is e3f2cae19743fcd2ee7452da25072bb3b4a639f9, which dates to April 27, 2017.
- Exception: The version of Rosetta that the DDG metric is currently running is 981ca1ab37cf1092da719de54cee4cfd8a73867e, released on July 23, 2015
- DDG is running another version because our most complete and thorough benchmarking results indicate that specific version has performed optimally, and newer versions have not been sufficiently tested to positively affirm their scientific quality for this specific application.
- The version of Rosetta underlying Cyrus Bench HM is 6d43786b5bf9572f7da090dff963244eb31ee1aa, which dates to November 23, 2016.
ROSETTA COMMANDS AND FLAGS:
- Prepare = Relax with these extra flags
- relax:constrain_relax_to_start_coords
- relax:coord_constrain_sidechains
- relax:ramp_constraints false
- Repack = Fixbb with flag
- repack_only
- Minimize = Minimize
- Relax = Fastrelax
- Loop Rebuild = Loopmodel (aka Next Generation KIC)
- loops:remodel perturb_kic
- loops:refine refine_kic
- kic_rama2b
- loops:ramp_fa_rep
- loops:ramp_rama
- kic_omega_sampling
- allow_omega_move true
- Design = Fixbb
- FlexDesign = Coupled_moves
- RelaxDesign = Fastdesign
- Epitope Scan = Rosetta_Scripts described here
- DDG = Ddg_monomer
- Antibody HM = RosettaAntibody3 with flags:
– name: num-out-models
value: 10
– name: exclude-homologs
value: false
– name: no-relax
value: false
– name: output-ab-scheme
value: Chothia_Scheme
GENERAL FLAGS:
- SCORE flag:
- score:weights talaris2013
- LIGAND flags:
- ignore_unrecognized_res false
- ignore_waters false
- load_PDB_components false
- PACKING flags:
- ex1
- ex2
- extrachi_cutoff 0
- use_input_sc
- ROTAMER flag:
- relax::limit_aroma_chi2 true