Mini rosetta command line option descriptions. (This is automatically generated file, do not edit!)

• in

  -in <Boolean>

  Input option group
  

  -termini <Boolean>

  Put full N and C termini on input structures
  Default: true
  

  -ignore_unrecognized_res <Boolean>

  Do not abort if unknown residues are found in PDB file; instead, ignore them.
  Default: false
  

  -remember_unrecognized_res <Boolean>

  Ignore unrecognized residues, but remember them in PDBInfo.
  Default: false
  

  -remember_unrecognized_water <Boolean>

  Remember waters along with other unrecognized residues.
  Default: false
  

  -detect_disulf <Boolean>

  Forcably enable or disable disulfide detection. When unspecified, rosetta conservatively detects disulfides in full atom input based on SG distance, but will not form centroid disulfides. Setting `-detect_disulf true` will force aggressive disulfide detection in centroid poses based on CB distance. Setting `-detect_disulf false` disables all detection, even in full atom poses. Note that disabling disulfides causes severe clashes for native disulfides.
  

  -fix_disulf <File>

  Specify disulfide connectivity via a file. Disulfides are specified as two whitespace-seperated residue indicies per line. This option replaces the old '-run:fix_disulf' option.
  

  -use_stupid_foldtree_format <Boolean>

  use the fold-tree format that existed for one week after revision 21447
  Default: false
  

  -target_residues <IntegerVector>

  which residue numbers to pass for getDistConstraints
  

• in:path

  -path <PathVector>

  Paths to search for input files (checked after type-specific paths)
  Default: "."
  

  -fragments <PathVector>

  Fragment file input search paths
  

  -pdb <PathVector>

  PDB file input search paths
  

  -database <PathVector>

  Database file input search paths. If the database is not found the ROSETTA3_DB environment variable is tried.
  

• in:file

  -file <Boolean>

  Input file option group
  

  -s <FileVector>

  Name(s) of single PDB file(s) to process
  

  -l <FileVector>

  File(s) containing list(s) of PDB files to process
  

  -list <FileVector>

  File(s) containing list(s) of PDB files. PDBs on the same line become one pose
  

  -native <File>

  Native PDB filename
  

  -torsion_bin_probs <File>

  File describing probabilities over torsion bins A,B,E,G,O
  Default: "empty"
  

  -talos_phi_psi <File>

  File that provides Phi-Psi angles in Talos+ format
  

  -talos_cs <File>

  File that provides chemical shifts in Talos format
  

  -ambig_talos_cs_A <File>

  File that provides 1st set of ambigious chemical shift options in Talos format
  

  -ambig_talos_cs_B <File>

  File that provides 2nd set of ambigious chemical shift options in Talos format
  

  -native_exclude_res <IntegerVector>

  Residue numbers to be excluded from RMS calculation
  

  -tags <StringVector>

  Tag(s) of structures to be used from silent-file
  

  -user_tags <StringVector>

  user_tag(s) of structures to be used from silent-file
  

  -tagfile <File>

  file with list of tags to be resampled from file given with in:resample:silent
  Default: "TAGS"
  

  -frag_files <FileVector>

  Fragment input file names
  

  -frag_sizes <IntegerVector>

  Fragment file sizes
  

  -extra_res_fa <FileVector>

  .params file(s) for new fullatom residue types (e.g. ligands)
  

  -extra_res_mol <FileVector>

  .mol file(s) for new fullatom residue types (e.g. ligands)
  

  -extra_res_cen <FileVector>

  .params file(s) for new centroid residue types (e.g. ligands)
  

  -extra_res_path <PathVector>

  directories with .params files. Only files containing 'param' will be chosen
  

  -frag3 <String>

  No description
  

  -frag9 <String>

  No description
  

  -fragA <String>

  No description
  

  -fragB <String>

  No description
  

  -xyz <String>

  Input coordinates in a raw XYZ format (three columns)
  

  -fragA_size <Integer>

  No description
  Default: 9
  

  -keep_input_scores <Boolean>

  Keep/Don't Keep scores from input file in Pose.
  Default: true
  

  -silent <FileVector>

  silent input filename(s)
  

  -atom_tree_diff <FileVector>

  atom_tree_diff input filename(s)
  

  -zip <String>

  zipped input file, used for BOINC database
  

  -boinc_wu_zip <FileVector>

  zipped input file with files for a specific BOINC workunit
  

  -fullatom <Boolean>

  Enable full-atom input of PDB or centroid structures
  Default: false
  

  -residue_type_set <String>

  ResidueTypeSet for input files
  Default: "fa_standard"
  

  -pca <File>

  compute PCA projections
  Default: ""
  

  -silent_energy_cut <Real>

  energy cut for silent-files
  Default: 1.0
  

  -silent_list <FileVector>

  Silent input filename list(s) - like -l is to -s
  

  -silent_renumber <Boolean>

  renumber decoys in not_universal_main or not
  Default: false
  

  -silent_optH <Boolean>

  Call optH when reading a silent file
  

  -silent_struct_type <String>

  Type of SilentStruct object to use in silent-file input
  Default: "protein"
  

  -silent_read_through_errors <Boolean>

  will ignore decoys with errors and continue reading
  Default: false
  

  -silent_score_prefix <String>

  Prefix that is appended to all scores read in from a silent-file
  Default: ""
  

  -silent_select_random <Integer>

  Select a random subset of this number of decoys from every silent-file read
  Default: 0
  

  -silent_scores_wanted <StringVector>

  Only put these silent-scores into the Pose.
  

  -centroid_input <Boolean>

  Enable centroid inputs of PDBs
  Default: false
  

  -fasta <FileVector>

  Fasta-formatted sequence file
  

  -pssm <FileVector>

  NCBI BLAST formatted position-specific scoring matrix
  

  -checkpoint <File>

  Sequence profile (binary file format) prepared by NCBI BLAST
  

  -alignment <FileVector>

  Input file for sequence alignment
  

  -alignment2 <FileVector>

  Input file for second sequence alignment
  

  -rama2b_map <File>

  Ramachandran file used by rama2b
  Default: "Rama08.dat"
  

  -psipred_ss2 <File>

  psipred_ss2 secondary structure definition file
  Default: "tt"
  

  -dssp <File>

  dssp secondary structure definition file
  Default: "tt"
  

  -fail_on_bad_hbond <Boolean>

  exit if a hydrogen bonding error is detected
  Default: true
  

  -movemap <File>

  No description
  Default: "default.movemap"
  

  -repair_sidechains <Boolean>

  attempt a repack/minmize to repair sidechain problems, such as proline geometry and his tautomerization
  Default: false
  

  -no_binary_dunlib <Boolean>

  Do not attempt to read from or write to a binary file for the Dunbrack library
  

  -extended_pose <Integer>

  number of extended poses to process in not_universal_main
  Default: 1
  

  -template_pdb <FileVector>

  Name of input template PDB files for comparative modeling
  

  -template_silent <File>

  input templates for comparative modeling -- tag needs to fit alignment id
  

  -rdc <FileVector>

  Experimental NMR Residual Dipolar Coupling File --- one file per alignment medium
  

  -vall <FileVector>

  Fragment database file, e.g vall.dat.2006-05-05
  Default: "filtered.vall.dat.2006-05-05"
  

  -rescore <Boolean>

  Governs whether input poses are rescored or not in not_universal_main, defaults to false.
  Default: false
  

  -spanfile <String>

  Membrane spanning file
  

  -lipofile <String>

  Membrane exposure file
  

  -sucker_params <File>

  Parameter file containing SplineEnergy parameters
  Default: "scoring/spline_energy_functions/sucker.params"
  

  -fold_tree <File>

  User defined fold tree to be imposed on the pose after reading from disk
  

  -obey_ENDMDL <Boolean>

  Stop reading a PDB after ENDMDL card; effectively read only first model in multimodel NMR PDBs
  Default: false
  

  -new_chain_order <Boolean>

  ensures chain from different MODEL records have differnet mini chains
  Default: false
  

• in:rdf

  -rdf <Boolean>

  rdf option group
  

  -sep_bb_ss <Boolean>

  separate RDFs by SS for backbone atypes
  Default: true
  

• MM

  -MM <Boolean>

  MM option group
  

  -ignore_missing_bondangle_params <Boolean>

  ignore failed lookups for missing bond angle parameters
  Default: false
  

• qsar

  -qsar <Boolean>

  qsar option group
  

  -weights <String>

  select qsar weight set to use
  Default: "standard"
  

• residues

  -residues <Boolean>

  residues option group
  

  -patch_selectors <StringVector>

  allow patch files that have CMDLINE_SELECTOR tags can be switched on with this option
  

• PCS

  -PCS <Boolean>

  PCS option group
  

  -write_extra <File>

  Write into the File PCS calc, PCS exp, PCS dev, tensor informations, AT EACH ENERGY EVALUATION. More suited for rescoring
  

  -normalization_id <Integer>

  Normalize individual data set. The integer identify the normalization method to be used
  

• inout

  -inout <Boolean>

  Ouput option group
  

  -fold_tree_io <Boolean>

  Ignore 'CHECKPOINT' file and the overwrite the PDB file(s)
  

• out

  -out <Boolean>

  Ouput option group
  

  -overwrite <Boolean>

  Ignore 'CHECKPOINT' file and the overwrite the PDB file(s)
  

  -nstruct <Integer>

  Number of times to process each input PDB
  Default: 1
  

  -shuffle_nstruct <Integer>

  total number of decoys to produce
  Default: 1
  

  -prefix <String>

  Prefix for output structure names, like old -series code
  Default: ""
  

  -suffix <String>

  Suffix for output structure names
  Default: ""
  

  -pdb_gz <Boolean>

  Compress (gzip) output pdbs
  Default: false
  

  -pdb <Boolean>

  Output PDBs
  Default: false
  

  -silent_gz <Boolean>

  Use gzipped compressed output (silent run level)
  Default: false
  

  -nooutput <Boolean>

  Surpress outputfiles
  Default: false
  

  -output <Boolean>

  Force outputfiles
  Default: false
  

  -scorecut <Real>

  Only output lowest energy fraction of structures - default 1.0, i.e. output all
  Default: 1.0
  

  -show_accessed_options <Boolean>

  In the end of the run show options that has been accessed.
  Default: false
  

  -sf <File>

  filename for score output
  Default: "score.fsc"
  

  -mute <StringVector>

  Mute specified Tracer chanels, specify 'all' to mute all chanels
  

  -unmute <StringVector>

  UnMute specified Tracer chanels, specify 'all' to mute all chanels
  

  -level <Integer>

  Level of Tracer output, any level above will be muted. Availible levels: 0 - fatal, 100 - error, 200 - warning, 300 - info, 400 - debug, 500 - trace. For additional info please see: src/core/util/Tracer.hh and doc page 'Tracer, tool for debug IO'. Default output level is 'info': 300
  Default: 300
  

  -mute_warning <StringVector>

  Mute specified Tracer chanels for msgs with priority warning and less
  

  -mute_info <StringVector>

  Mute specified Tracer channels for msgs with priority info and less
  

  -mute_debug <StringVector>

  Mute specified Tracer channels for msgs with priority debug and less
  

  -unmute_error <StringVector>

  Unmute specified Tracer channels for msgs of priority ERROR and more
  

  -unmute_warning <StringVector>

  Unmute specified Tracer chanels for msgs with priority warning and more
  

  -unmute_info <StringVector>

  Unmute specified Tracer channels for msgs with priority info and more
  

  -unmute_debug <StringVector>

  Unmute specified Tracer channels for msgs with priority debug and more
  

  -chname <Boolean>

  Add Tracer chanel names to output
  Default: true
  

  -dry_run <Boolean>

  If set ComparingTracer will not generate any asserts, and save all Tracer output to a file
  Default: false
  

  -mpi_tracer_to_file <String>

  MPI ONLY: Redirect all tracer output to this file with '_<mpi_rank>' appened as a suffix
  Default: "tracer.out"
  

  -user_tag <String>

  add this tag to structure tags: e.g., a process id
  Default: ""
  

  -output_tag <String>

  Prefix output files with this tag, if code checks for it
  Default: ""
  

• out:file

  -file <Boolean>

  Output file option group
  

  -o <String>

  Name of output file
  

  -silent <String>

  Use silent file output, use filename after this flag
  Default: "default.out"
  

  -score_only <String>

  Only output scores, no silent files or pdb files
  Default: "default.sc"
  

  -atom_tree_diff <String>

  Use atom_tree_diff file output, use filename after this flag
  Default: "default.out"
  

  -alignment <String>

  Output file for sequence alignment
  Default: "out.align"
  

  -scorefile <String>

  Write a scorefile to the provided filename
  Default: "default.sc"
  

  -silent_struct_type <String>

  Type of SilentStruct object to use in silent-file output
  Default: "protein"
  

  -silent_preserve_H <Boolean>

  Preserve hydrogrens in PDB silent-file format.
  Default: false
  

  -silent_print_all_score_headers <Boolean>

  Print a SCORE header for every SilentStruct in a silent-file
  Default: false
  

  -silent_decoytime <Boolean>

  Add time since last silent structure was written to score line
  Default: false
  

  -silent_comment_bound <Integer>

  String data longer than this ends up as remark rather than in score line
  Default: 15
  

  -raw <Boolean>

  Use silent-type file output
  Default: false
  

  -fullatom <Boolean>

  Enable full-atom output of PDB or centroid structures
  Default: false
  

  -output_virtual <Boolean>

  Output virtual atoms in output of PDB
  Default: false
  

  -weight_silent_scores <Boolean>

  weight scores in silent-file output.
  Default: true
  

  -design_contrast <File>

  output list comparing design sequence to native sequence
  Default: "redesign"
  

  -dont_rewrite_dunbrack_database <Boolean>

  disables the default behavior of rewriting the dunrack library in binary format if a binary version is not found
  

  -renumber_pdb <Boolean>

  use Rosetta residue numbering and arbitrary chain labels in pdb output
  Default: false
  

  -pdb_parents <Boolean>

  If the pose contains a comment named template print this as a REMARK in the pdb file
  Default: false
  

  -per_chain_renumbering <Boolean>

  when used in conjunction with renumber_pdb, restarts residue numbering at each chain
  Default: false
  

  -residue_type_set <String>

  ResidueTypeSet for output files
  Default: "fa_standard"
  

  -frag_prefix <String>

  Prefix for fragment output
  Default: "default.frags"
  

• out:path

  -all <Path>

  Default file output path
  Default: "."
  

  -path <Path>

  Default file output path
  Default: "."
  

  -pdb <Path>

  PDB file output path
  

  -score <Path>

  Score file output path
  

  -movie <Path>

  Movie file output path
  

  -scratch <Path>

  use this path as scratch drive
  Default: ['"/scratch/USERS/"']
  

  -mpi_rank_dir <Boolean>

  put silent-output files in individual directory as determined by mpi-rank
  Default: false
  

• pocket_grid

  -pocket_grid <Boolean>

  pocket_grid option group
  

  -pocket_grid_size <Real>

  grid spacing in Angstroms
  Default: 0
  

  -pocket_grid_size_x <Real>

  grid spacing in Angstroms
  Default: 10
  

  -pocket_grid_size_y <Real>

  grid spacing in Angstroms
  Default: 10
  

  -pocket_grid_size_z <Real>

  grid spacing in Angstroms
  Default: 10
  

  -pocket_grid_spacing <Real>

  grid spacing in Angstroms
  Default: 0.5
  

  -pocket_max_spacing <Real>

  Maximum residue-residue distance to be considered a pocket
  Default: 8
  

  -pocket_min_size <Real>

  Minimum pocket size to score, in cubic Angstroms
  Default: 10
  

  -pocket_max_size <Real>

  Maximum pocket size to report, in cubic Angstroms, 0 for no limit
  Default: 0
  

  -pocket_probe_radius <Real>

  radius of surface probe molecule
  Default: 1.0
  

  -central_relax_pdb_num <String>

  Residue number:(optional)Chain around which to do Pocket Constraint
  Default: "-1"
  

  -pocket_ntrials <Integer>

  Number of trials to use for backrub
  Default: 100000
  

  -pocket_side <Boolean>

  Include only side chain residues for target surface
  Default: false
  

  -pocket_dump_pdbs <Boolean>

  Generate PDB files
  Default: false
  

  -pocket_dump_rama <Boolean>

  Generate Ramachandran maps for each pocket cluster
  Default: false
  

  -pocket_restrict_size <Boolean>

  Pockets that are too large return score of 0
  Default: false
  

  -pocket_psp <Boolean>

  Mark Pocket-Solvent-Pocket events as well
  Default: true
  

  -pocket_sps <Boolean>

  Unmark Solvent-Pocket-Solvent events
  Default: false
  

  -pocket_surface_score <Real>

  Score given to pocket surface
  Default: 0
  

  -pocket_surface_dist <Real>

  Distance to consider pocket surface
  Default: 2.5
  

  -pocket_buried_score <Real>

  Score given to deeply buried pocket points
  Default: 5.0
  

  -pocket_buried_dist <Real>

  Distance to consider pocket buried
  Default: 2.0
  

• fingerprint

  -fingerprint <Boolean>

  fingerprint option group
  

  -atom_radius_scale <Real>

  Scale to shrink the radius of atom
  Default: 0.9
  

  -atom_radius_buffer <Real>

  Value to subtract from all atomic radii, to match PocketGrid buffer thickness
  Default: 1.0
  

  -packing_weight <Real>

  Add weight to rho large deviation
  Default: 1
  

  -dist_cut_off <Real>

  set cut_off distance to add packing weight
  Default: 5
  

• docking

  -kick_relax <Boolean>

  Add relax step at the end of symmetric docking
  Default: false
  

  -docking <Boolean>

  Docking option group
  

  -view <Boolean>

  Decide whether to use the viewer (graphical) or not
  Default: false
  

  -no_filters <Boolean>

  Toggle the use of filters
  Default: false
  

  -design_chains <StringVector>

  Pass in the one-letter chain identifiers, separated by space, for each chain to design: -design_chains A B
  

  -partners <String>

  defines docking partners by ChainID, example: docking chains L+H with A is -partners LH_A
  Default: "_"
  

  -docking_local_refine <Boolean>

  Do a local refinement of the docking position (high resolution)
  Default: false
  

  -low_res_protocol_only <Boolean>

  Run only low resolution docking, skip high resolution docking
  Default: false
  

  -randomize1 <Boolean>

  Randomize the first docking partner.
  Default: false
  

  -randomize2 <Boolean>

  Randomize the second docking partner.
  Default: false
  

  -spin <Boolean>

  Spin a second docking partner around axes from center of mass of partner1 to partner2
  Default: false
  

  -dock_pert <RealVector>

  Do a small perturbation with partner two: -dock_pert ANGSTROMS DEGREES. Good values for protein docking are 3 A and 8 deg.
  

  -uniform_trans <Real>

  No description
  

  -docking_centroid_outer_cycles <Integer>

  Outer cycles during cking rigid body adaptive moves.
  Default: 10
  

  -docking_centroid_inner_cycles <Integer>

  Inner cycles during docking rigid body adaptive moves.
  Default: 50
  

  -dock_min <Boolean>

  Minimize the final fullatom structure.
  Default: false
  

  -flexible_bb_docking <String>

  How to do flexible backbone docking, if at all. Choices include fixedbb, ccd, alc, and backrub.
  Default: "fixedbb"
  

  -flexible_bb_docking_interface_dist <Real>

  Distance between chains required to define a residue as having flexible backbone (ie. loop).
  Default: 10.0
  

  -ensemble1 <String>

  turns on ensemble mode for partner 1. String is multi-model pdb file
  Default: ""
  

  -ensemble2 <String>

  turns on ensemble mode for partner 2. String is multi-model pdb file
  Default: ""
  

  -dock_mcm_trans_magnitude <Real>

  The magnitude of the translational perturbation during mcm in docking.
  Default: 0.1
  

  -dock_mcm_rot_magnitude <Real>

  The magnitude of the rotational perturbation during mcm in docking.
  Default: 5.0
  

  -dock_rtmin <Boolean>

  does rotamer trials with minimization, RTMIN
  Default: false
  

  -sc_min <Boolean>

  does sidechain minimization of interface residues
  Default: false
  

  -norepack1 <Boolean>

  Do not repack the side-chains of partner 1.
  Default: false
  

  -norepack2 <Boolean>

  Do not repack the side-chains of partner 2.
  Default: false
  

  -dock_ppk <Boolean>

  docking prepack mode
  Default: false
  

  -max_repeats <Integer>

  If a decoy does not pass the low- and high-resolution filters, how many attempts to make before failur
  Default: 1000
  

  -dock_lowres_filter <RealVector>

  manually sets the lowres docking filter: -dock_lowres_filter <INTERCHAIN_CONTACT cutoff>=""> <INTERCHAIN_VDW cutoff>="">. Default values for protein docking are 10.0 and 1.0
  

  -multibody <IntegerVector>

  List of jumps allowed to move during docking
  

  -low_patch <String>

  Name of weights patch file (without extension .wts) to use during rigid body
  

  -high_patch <String>

  Name of weights patch file (without extension .wts) to use during docking
  

  -high_min_patch <String>

  Name of weights patch file (without extension .wts) to use during
  

  -pack_patch <String>

  Name of weights patch file (without extension .wts) to use during packing
  

  -use_new_protocol <Boolean>

  Use the new high resolution docking algorithm that is currently undergoing testing.
  Default: true
  

• docking:ligand

  -ligand <Boolean>

  docking:ligand option group
  

  -protocol <String>

  Which protocol to run?
  Default: "abbreviated"
  

  -soft_rep <Boolean>

  Use soft repulsive potential?
  Default: false
  

  -old_estat <Boolean>

  Emulate Rosetta++ electrostatics? (higher weight, ignore protein-protein)
  Default: false
  

  -random_conformer <Boolean>

  Start from a random ligand rotamer chosen from the library
  Default: false
  

  -improve_orientation <Integer>

  Do N cycles of randomization to minimize clashes with backbone
  

  -mutate_same_name3 <Boolean>

  Allow ligand to 'design' to residue types with same name3? Typically used for protonation states / tautomers.
  Default: false
  

  -min_rms <Real>

  When selecting a subset of ligand poses, all must differ by at least this amount.
  Default: 0.8
  

  -max_poses <Integer>

  When selecting a subset of ligand poses, select as most this many.
  Default: 50
  

  -minimize_ligand <Boolean>

  Allow ligand torsions to minimize?
  Default: false
  

  -harmonic_torsions <Real>

  Minimize with harmonic restraints with specified stddev (in degrees)
  Default: 10.0
  

  -use_ambig_constraints <Boolean>

  Use ambiguous constraints to restrain torsions instead of adding and removing constraints
  Default: false
  

  -shear_moves <Integer>

  Do N pseudo-shear moves on ligand torsions per MCM cycle
  Default: 0
  

  -minimize_backbone <Boolean>

  Allow protein backbone to minimize? Restrained except near ligand.
  Default: false
  

  -harmonic_Calphas <Real>

  Minimize with harmonic restraints with specified stddev (in Angstroms)
  Default: 0.2
  

  -tether_ligand <Real>

  Restrain ligand to starting point with specified stddev (in Angstroms)
  

  -start_from <RealVector>

  One or more XYZ locations to choose for the ligand: -start_from X1 Y1 Z1 -start_from X2 Y2 Z2 ...
  

• docking:ligand:grid

  -grid <Boolean>

  docking:ligand:grid option group
  

  -grid_kin <File>

  Write kinemage version of generated grid to named file
  

  -grid_map <File>

  Write grid to named file as electron density in BRIX (aka `O'-map) format
  

• docking:ligand

  -option_file <String>

  Name of Ligand Option File for use with multi_ligand_dock application
  

  -rescore <Boolean>

  No docking (debug/benchmark mode)
  Default: false
  

• docking:symmetry

  -symmetry <Boolean>

  symmetry option group
  

  -minimize_backbone <Boolean>

  Allow protein backbone to minimize?
  Default: false
  

  -minimize_sidechains <Boolean>

  Allow protein sidechains to minimize?
  Default: false
  

• pH

  -pH <Boolean>

  pH option group
  

  -pH_mode <Boolean>

  Allow protonated/deprotonated versions of the residues based on pH
  Default: false
  

  -value_pH <Real>

  pH value input for the pHEnergy score
  Default: 7.0
  

• pH:calc_pka

  -calc_pka <Boolean>

  calc_pka option group
  

  -pka_for_resno <Integer>

  Residue no whose pKa value is to be determined
  Default: -1
  

  -pka_for_chainno <String>

  Chain no of the residue whose pKa is to be determined
  Default: "A"
  

• run

  -run <Boolean>

  Run option group
  

  -batches <FileVector>

  batch_flag_files
  Default: ""
  

  -no_prof_info_in_silentout <Boolean>

  no time-columns appears in score/silent - files
  Default: false
  

  -archive <Boolean>

  run MPIArchiveJobDistributor
  Default: false
  

  -shuffle <Boolean>

  Shuffle job order
  Default: false
  

  -n_cycles <Integer>

  Option to control miscellaneous cycles within protocols. This has no core meaning - it is meant to reduce option-bloat by having every protocol define separate cycles options. Check your protocol's documentation to see if it is used.
  Range: 1-
  Default: 1
  

  -repeat <Integer>

  Repeat mover N times
  Range: 0-
  Default: 1
  

  -max_min_iter <Integer>

  Maximum number of iterations of dfpmin
  Default: 200
  

  -maxruntime <Integer>

  Maximum runtime in seconds. JobDistributor will signal end if time is exceeded no matter how many jobs were finished.
  Default: -1
  

  -write_failures <Boolean>

  write failed structures to output
  Default: false
  

  -clean <Boolean>

  clean input pdb befere processing them
  Default: false
  

  -benchmark <Boolean>

  Run in benchmark mode
  

  -test_cycles <Boolean>

  When running tests, use reduced cycles. Cycles must be defined in the code itself
  Default: false
  

  -benchmark_scale <Integer>

  Run in benchmark mode
  Default: 1
  

  -dry_run <Boolean>

  Run through structures/tasks/etc skipping the actual calculation step for testing of I/O and/or setup
  Default: false
  

  -debug <Boolean>

  Run in debug mode
  

  -profile <Boolean>

  Run in profile mode
  Default: false
  

  -max_retry_job <Integer>

  If a job fails with FAIL_RETRY retry this many times at most
  Default: 10
  

  -verbosity <Integer>

  Logging verbosity level
  Range: 0-9
  Default: 0
  

  -version <Boolean>

  write out SVN version info, if it was available at compile time
  Default: true
  

  -nodelay <Boolean>

  Do not delay launch of minirosetta
  

  -delay <Integer>

  Wait N seconds before doing anything at all. Useful for cluster job staggering.
  Default: 0
  

  -random_delay <Integer>

  Wait a random amount of 0..N seconds before doing anything at all. Useful for cluster job staggering.
  Default: 0
  

  -timer <Boolean>

  write out time per decoy in minutes in scorefile
  

  -series <String>

  alternate way to specify the code name chain
  Default: "ss"
  

  -protein <String>

  protein <pdbcode> these options override the first three args
  Default: "----"
  

  -chain <String>

  -chain <chain_id>
  Default: "-"
  

  -score_only <Boolean>

  calculate the score only and exit
  Default: false
  

  -silent_input <Boolean>

  read start structures from compressed format requires -refold -s <.out file> -l <label/index list file> or use -all in place of -l

  use all files
  

  -decoystats <Boolean>

  calculate values of a series of additional structural properties, including counting unsatisfied buried Hbond donors and acceptors, SASApack, etc. Additional output associated with this flag is written both to stdout and to output PDB files
  

  -output_hbond_info <Boolean>

  print hydrogen bond info in the stats section of written out PDB files
  

  -wide_nblist_extension <Real>

  Amount to extend the wide neighbor list
  Default: 2.0
  

  -status <Boolean>

  Generate a status file
  

  -constant_seed <Boolean>

  Use a constant seed (1111111 unless specified)
  

  -jran <Integer>

  Specify seed (requires -constant_seed)
  Default: 1111111
  

  -use_time_as_seed <Boolean>

  Use time as random number seed instead of default rng seed device.
  

  -rng_seed_device <String>

  Obtain random number seed from specified device.
  Default: "/dev/urandom"
  

  -seed_offset <Integer>

  This value will be added to the random number seed. Useful when using time as seed and submitting many jobs to clusters. Using the condor job id will force jobs that are started in the same second to still have different initial seeds
  Default: 0
  

  -rng <String>

  Random number generation algorithm: Currently only mt19937 is a accepted here
  Default: "mt19937"
  

  -run_level <Integer>

  Specify runlevel by integer
  Default: 0
  

  -verbose <String>

  Keyword runlevels (decreasing verbosity): gush yap chat inform quiet silent
  

  -silent <Boolean>

  use compressed output (also a runlevel)
  

  -regions <Boolean>

  Specify regions of the protein allowed to move
  

  -find_disulf <Boolean>

  Each time the pose is scored, attempt to find new disulfide bonds.
  Default: false
  

  -rebuild_disulf <Boolean>

  Attempt to build correct disulfide geometry when converting from a centroid pose to a full atom pose. Disulfides must be previously annotated, either by enabling -detect_disulf or by specifying a file to -fix_disulf.
  Default: false
  

  -movie <Boolean>

  Update _movie.pdb file for rasmol_rt
  

  -trajectory <Boolean>

  Write a pdb file of each accepted structure
  

  -IUPAC <Boolean>

  Use IUPAC hydrogen conventions in place of PDB conventions
  

  -preserve_header <Boolean>

  Maintain header info from input PDB when writing output PDBs
  

  -evolution <Boolean>

  evolutionary algorithm applied to fullatom refinement of structure models
  

  -suppress_checkpoints <Boolean>

  Override & switch off checkpoints.
  

  -checkpoint <Boolean>

  Turn checkpointing on
  

  -delete_checkpoints <Boolean>

  delete the checkpoints after use
  Default: true
  

  -checkpoint_interval <Integer>

  Checkpoint time interval in seconds
  Range: 10-
  Default: 600
  

  -protocol <String>

  Which protocol to run, for Rosetta wrapper
  Default: "abrelax"
  

  -remove_ss_length_screen <Boolean>

  Sets the use_ss_length_screen flag in the Fragment Mover to false
  

  -min_type <String>

  type of minimizer to use
  Default: "dfpmin"
  

  -min_tolerance <Real>

  minimizer tolerance
  Default: 0.000001
  

  -nblist_autoupdate <Boolean>

  Turn on neighborlist auto-updates for all minimizations
  Default: false
  

  -nblist_autoupdate_narrow <Real>

  With nblist autoupdate: the reach in Angstroms for the narrow neighbor list
  Default: 0.5
  

  -nblist_autoupdate_wide <Real>

  With nblist autoupdate: the reach in Angstroms for the wide neighbor list
  Default: 2.0
  

  -skip_set_reasonable_fold_tree <Boolean>

  Do not run set_reasonable_fold_tree when creating a pose from a pdb. Useful for unreasonable PDBs where the user sets a fold tree explicitly.
  Default: false
  

  -randomize_missing_coords <Boolean>

  Insert random coordinates for missing density atoms ( occupancy is zero ) and for any atoms with negative occupancy, randomizing coords is done by default
  Default: false
  

  -trust_missing_coords <Boolean>

  keep coords information for missing density atoms ( occupancy is zero ) defined in input structures
  Default: false
  

  -cycles_outer <Integer>

  number of outer cycles
  Range: 1-
  Default: 1
  

  -cycles_inner <Integer>

  number of inner cycles
  Range: 1-
  Default: 1
  

  -repack_rate <Integer>

  repack after every [value] cycles during certain protocols
  Range: 1-
  Default: 10
  

  -reinitialize_mover_for_each_job <Boolean>

  job distributor will generate fresh copy of its mover before each apply (once per job)
  Default: false
  

  -reinitialize_mover_for_new_input <Boolean>

  job distributor will generate fresh copy of its mover whenever the pose being passed to the mover is going to change (e.g., next PDB in -l)
  Default: false
  

  -multiple_processes_writing_to_one_directory <Boolean>

  activates .in_progress files used to communicate between independent processes that a job is underway. UNSAFE but may be convenient.
  Default: false
  

  -jobdist_miscfile_ext <String>

  extension for JobOutputter file() function (miscellaneous file output).
  Default: ".data"
  

  -no_scorefile <Boolean>

  do not output scorefiles
  Default: false
  

  -other_pose_to_scorefile <Boolean>

  write other_pose (JobOutputter) to a scorefile; path by other_pose_scorefile; be warned you can get garbage if scorefunctions for poses do not match. Overridden by no_scorefile
  Default: false
  

  -other_pose_scorefile <File>

  Path to other_pose (JobOutputter) scorefiles. Default is same scorefile as regular result poses. The default will cause problems if your output poses were scored on different scorefunctions.
  Default: ""
  

  -intermediate_scorefiles <Boolean>

  write intermediate evaluations to disk (depends on your protocol if and how often this happens
  Default: false
  

  -intermediate_structures <Boolean>

  write structures together with intermediate evaluations
  Default: false
  

  -idealize_before_protocol <Boolean>

  run idealize first, before running whatever.
  

  -interactive <Boolean>

  Signal Rosetta is to be run as a library in an interactive application. In particular, favor throwing exceptions on bad inputs rather than exiting.
  Default: false
  

  -condor <Boolean>

  if condor say yes -- proc_id counting starts at 0
  Default: false
  

  -nproc <Integer>

  number of process... needed if proc_id is specified
  Default: 0
  

  -proc_id <Integer>

  give process number... Jobdistributor will only work on proc_id mod nproc part of work
  Default: 0
  

  -exit_if_missing_heavy_atoms <Boolean>

  quit if heavy atoms missing in pdb
  Default: false
  

• jd2

  -jd2 <Boolean>

  jd2 option group
  

  -mpi_nowait_for_remaining_jobs <Boolean>

  exit immediately (not graceful -- not complete) if the last job has been sent out
  Default: false
  

  -mpi_work_partition_job_distributor <Boolean>

  determine if we should use the WorkPartition job distributor
  Default: false
  

  -mpi_file_buf_job_distributor <Boolean>

  determine if we should use the MPIFileBufJobDistributor (warning: silent output only)
  Default: true
  

  -mpi_filebuf_jobdistributor <Boolean>

  same as mpi_file_buf_job_distributor but with more intuitive spacing... determine if we should use the MPIFileBufJobDistributor (warning: silent output only)
  Default: true
  

  -mpi_fast_nonblocking_output <Boolean>

  By default the master node blocks while a slave node outputs to avoid two slaves writing to a score file or silent file at the same time setting this to true disables that feature
  Default: false
  

  -dd_parser <Boolean>

  determine whether to use the dock_design_parser
  Default: false
  

  -ntrials <Integer>

  number of attempts at creating an output file for each nstruct. e.g., ntrials 3 and nstruct 10 would mean that each of 10 trajectories would attempt to write an output file 3 times and if unsuccessful would fail.
  

  -generic_job_name <String>

  job name when using GenericJobInputter (i.e. abinitio)
  Default: "S"
  

  -no_output <Boolean>

  use NoOutputJobOutputter; do not store the pose after a run (no silent or scorefile)
  Default: false
  

  -enzdes_out <Boolean>

  causes an enzdes-style scorefile (with information about catalytic res and some pose metric stuff ) to be written instead of the regular scorefile
  Default: false
  

  -buffer_silent_output <Integer>

  write structures to silent-files in blocks of N structures to
  Default: 1
  

• evaluation

  -evaluation <Boolean>

  evaluation option group
  

  -rmsd_target <FileVector>

  [vector] determine rmsd against this/these structure(s)
  

  -rmsd_column <StringVector>

  [vector] use xxx as column name: rms_xxx
  

  -rmsd_select <FileVector>

  [vector] a bunch of loop files which makes rmsds with tags: rms_XXX, where XXX is basename of file
  

  -align_rmsd_target <FileVector>

  [vector] determine rmsd against this/these structure(s) using simple sequence alignment
  

  -align_rmsd_column <StringVector>

  [vector] use xxx as column name for align_rmsd_target: rms_xxx
  

  -align_rmsd_fns <FileVector>

  [vector] of sequence alignments used for align_rmsd files
  

  -align_rmsd_format <String>

  format for sequence alignment between structures used in evaluation
  Default: "grishin"
  

  -pool <File>

  find closest matching structure in this pool and report tag and rmsd
  

  -rmsd <FileVector>

  [vector/pairs] tripletts: rmsd_target (or NATIVE / IRMS) col_name selection_file (or FULL)
  

  -gdtmm <Boolean>

  for each rmsd evaluator also a gdtmm evaluator is created
  Default: false
  

  -score_with_rmsd <Boolean>

  score the pose on the same subset of atoms as in the rmsd poses
  

  -constraints <FileVector>

  [vector] evaluate against these constraint sets
  

  -constraints_column <FileVector>

  [vector] use xxx as column name: cst_xxx
  

  -combined_constraints <FileVector>

  [vector] use xxx as cst-file but combine constraints before applying
  

  -combined_constraints_column <FileVector>

  [vector] use xxx as cst-file but combine constraints before applying
  

  -combine_statistics <Integer>

  repeat constraint evaluation X times to get statistics of constraint combination
  Default: 10
  

  -chemical_shifts <StringVector>

  compute chemical shift score with SPARTA+ use tuples: talos_file [cs]_column_name (ATTENTION uses filesystem)
  

  -sparta_dir <String>

  [optional] point to an external resource for the sparta directory (instead of minirosetta_database)
  Default: "SPARTA+"
  

  -cam_shifts <StringVector>

  compute chemical shift score with Camshift talos_file [cs]_column_name (ATTENTION uses filesystem)
  

  -pales <StringVector>

  compute Residual Dipolar Couplings using the PALES program (ATTENTION uses filesystem)
  

  -extra_score <FileVector>

  [vector] provide .wts files to generate extra columns
  

  -extra_score_patch <FileVector>

  [vector] provide .patch files, set NOPATCH for columns that are not patched
  

  -extra_score_column <StringVector>

  [vector] use xxx as column name: score_xxx
  

  -extra_score_select <FileVector>

  [vector] /rigid/ files for selection, use SELECT_ALL as placeholder
  

  -rdc_select <FileVector>

  [vector] as rmsd_select provide loop-file(RIGID) to compute RDC score on selected residues
  

  -rdc_target <FileVector>

  [vector] as rmsd_target/column provide PDB wih missing density to compute RDC score on selected residues
  

  -symmetric_rmsd <Boolean>

  calculate the rmsd symmetrically by checking all chain orderings
  

  -rdc_column <StringVector>

  [vector] column names for rdc_select
  

  -rdc <StringVector>

  [vector] rdc-files and column names for RDC calculation
  

  -jump_nr <Boolean>

  adds the JumpNrEvaluator for the nrjumps column
  Default: false
  

  -score_exclude_res <IntegerVector>

  Calculates a select_score column based on all residues not excluded by the command line vector
  

  -score_sscore_short_helix <Integer>

  defines the maximum length of a helix that is not scored if it terminates a loop
  Default: 5
  

  -score_sscore_maxloop <Integer>

  defines the maximum length of a loop that is still considered for the sscore - score
  Default: 3
  

  -rpf <Boolean>

  will compute RPF score with distance cutoff 5 and store in column rpf_score
  Default: false
  

• filters

  -filters <Boolean>

  filters option group
  

  -disable_all_filters <Boolean>

  turn off all centroid filters: RG, CO, and Sheet
  Default: false
  

  -disable_rg_filter <Boolean>

  turn off RG filter
  Default: false
  

  -disable_co_filter <Boolean>

  turn off contact order filter
  Default: false
  

  -disable_sheet_filter <Boolean>

  turn off sheet filter
  Default: false
  

  -set_pddf_filter <Real>

  Turns on PDDF filter with a given score cutoff
  Default: 5.0
  

• MonteCarlo

  -MonteCarlo <Boolean>

  MonteCarlo option group
  

  -temp_initial <Real>

  initial temperature for Monte Carlo considerations
  Range: 0.001-
  Default: 2
  

  -temp_final <Real>

  final temperature for Monte Carlo considerations
  Range: 0.001-
  Default: 0.6
  

• frags

  -frags <Boolean>

  frags option group
  

  -filter_JC <Boolean>

  Filter J-coupling values in the dynamic range
  Default: false
  

  -bounded_protocol <Boolean>

  makes the picker use bounded protocol to select fragments. This is teh default behavior
  Default: true
  

  -keep_all_protocol <Boolean>

  makes the picker use keep-all protocol to select fragments. The default is bounded protocol
  Default: false
  

  -quota_protocol <Boolean>

  quota protocol implies the use of a QuotaCollector and a QuotaSelelctor, no matter what user set up by other flags.
  Default: false
  

  -p_value_selection <Boolean>

  the final fragment selection will b based on p-value rather than on a total score for the given fragment
  Default: false
  

  -n_frags <Integer>

  number of fragments per position
  Default: 200
  

  -allowed_pdb <File>

  provides a text file with allowed PDB chains (five characters per entry, e.g.'4mbA'). Only these PDB chains from Vall will be used to pick fragments
  

  -ss_pred <StringVector>

  provides one or more files with secondary structure prediction (PsiPred SS2 format) , to be used by secondary structure scoring and quota selector. Each file name must be followed by a string ID.
  

  -denied_pdb <File>

  provides a text file with denied PDB chains (five characters per entry, e.g.'4mbA'). This way close homologs may be excluded from fragment picking.
  

  -frag_sizes <IntegerVector>

  sizes of fragments to pick from the vall
  Default: ['9', '3', '1']
  

  -write_ca_coordinates <Boolean>

  Fragment picker will store CA Cartesian coordinates in output fragment files. By default only torsion coordinates are stored.
  Default: false
  

  -annotate <Boolean>

  read the annotation from the rosetta++ fragment file
  Default: false
  

  -nr_large_copies <Integer>

  make N copies for each standard 9mer (or so) fragment
  Default: 1
  

  -n_candidates <Integer>

  number of fragment candidates per position; the final fragments will be selected from them
  Default: 200
  

  -write_rama_tables <Boolean>

  Fragment picker will spit out sequence specific ramachandran score tables for your viewing pleasure. These ramachandran tables are based on the secondary structure predictions fed into RamaScore, and you may occasionally want to look at what the program has defined.
  Default: false
  

  -rama_C <Real>

  Constant in RamaScore equation, command line is for optimization tests
  Default: 0.0
  

  -rama_B <Real>

  Constant in RamaScore equation, command line is for optimization tests
  Default: 1.0
  

  -sigmoid_cs_A <Real>

  Constant in CSScore equation, command line is for optimization tests
  Default: 4.0
  

  -sigmoid_cs_B <Real>

  Constant in CSScore equation, command line is for optimization tests
  Default: 5.0
  

  -seqsim_H <Real>

  Secondary structure type prediction multiplier, for use in fragment picking
  Default: 1.0
  

  -seqsim_E <Real>

  Secondary structure type prediction multiplier, for use in fragment picking
  Default: 1.0
  

  -seqsim_L <Real>

  Secondary structure type prediction multiplier, for use in fragment picking
  Default: 1.0
  

  -rama_norm <Real>

  Used to multiply rama table values after normalization, default (0.0) means use raw counts (unnormalized)
  Default: 0.0
  

  -describe_fragments <String>

  Writes scores for all fragments into a file
  Default: ""
  

• frags:scoring

  -scoring <Boolean>

  scoring option group
  

  -config <File>

  scoring scheme used for picking fragments
  Default: ""
  

  -profile_score <String>

  scoring scheme used for profile-profile comparison
  Default: "L1"
  

  -predicted_secondary <FileVector>

  provides one or more files with secondary structure prediction, to be used by secondary structure scoring and quota selector
  Default: ""
  

• frags:picking

  -picking <Boolean>

  picking option group
  

  -selecting_rule <String>

  the way how fragments are selected from candidates, e.g. QuotaSelector of BestTotalScoreSelector
  Default: "BestTotalScoreSelector"
  

  -quota_config_file <File>

  provides a configuration file for quota selector
  

  -annotate_fragments <Boolean>

  switches on the fragment annotating mechanism. Picking runs may be slower, but output contains more information
  

  -query_pos <IntegerVector>

  provide sequence position for which fragments will be picked. By default fragments are picked for the whole query sequence
  

• broker

  -broker <Boolean>

  broker option group
  

  -setup <FileVector>

  setup file for topology-broker
  Default: "NO_SETUP_FILE"
  

• chunk

  -chunk <Boolean>

  chunk option group
  

  -pdb2 <File>

  file for chunk2
  

  -loop2 <File>

  rigid region for chunk2
  

• abinitio

  -abinitio <Boolean>

  Ab initio mode
  

  -membrane <Boolean>

  will use the membrane abinitio protocol. sequential insertion of TMH
  Default: false
  

  -kill_hairpins <File>

  setup hairpin killing in score (kill hairpin file or psipred file)
  

  -kill_hairpins_frequency <Real>

  automated hairpin killing frequency (for use with psipred file)
  Default: 0.2
  

  -smooth_cycles_only <Boolean>

  Only smooth cycles in abinitio protocol
  Default: false
  

  -relax <Boolean>

  Do a relax after abinitio = abrelax ?
  

  -final_clean_relax <Boolean>

  Do a final relax without constraints
  

  -fastrelax <Boolean>

  Do a fastrelax after abinitio = abfastrelax ?
  

  -multifastrelax <Boolean>

  Do a fastrelax after abinitio = abfastrelax ?
  

  -debug <Boolean>

  No description
  Default: false
  

  -clear_pose_cache <Boolean>

  always clear extra-scores away before output
  Default: false
  

  -explicit_pdb_debug <Boolean>

  always dump pdb (not silent ) files during abinitio stages
  Default: false
  

  -use_filters <Boolean>

  use RG, contact-order and sheet filters
  Default: false
  

  -increase_cycles <Real>

  Increase number of cycles at each stage of fold_abinitio (or pose_abinitio) by this factor
  Range: 0.001-
  Default: 1.0
  

  -number_3mer_frags <Integer>

  Number of top 3mer fragments to use in fold_abinitio protocol
  Range: 0-
  Default: 200
  

  -number_9mer_frags <Integer>

  Number of top 9mer fragments to use in fold_abinitio protocol
  Range: 0-
  Default: 25
  

  -temperature <Real>

  Temperature used in fold_abinitio
  Default: 2.0
  

  -rg_reweight <Real>

  Reweight contribution of radius of gyration to total score by this scale factor
  Default: 1.0
  

  -strand_dist_cutoff <Real>

  Specify distance cutoff (in Angstroms) between strand dimers within which they are called paired
  Default: 6.5
  

  -stretch_strand_dist_cutoff <Boolean>

  Allow strand distance cutoff to change from 6.5 A to a larger value (specified by '-max_strand_dist_cutoff <float>') linearly scaled according to sequence separation over a range specified by '-seq_sep_scale <float>'
  

  -rsd_wt_helix <Real>

  Reweight env,pair,cb for helix residues by this factor
  Default: 1.0
  

  -rsd_wt_strand <Real>

  Reweight env,pair,cb for strand residues by this factor
  Default: 1.0
  

  -rsd_wt_loop <Real>

  Reweight env,pair,cb for loop residues by this factor
  Default: 1.0
  

  -fast <Boolean>

  Runs protocol without minimization or gradients, giving a significant speed advantage For NOE data only, -fast yields essentially the protocol published by Bowers et al., JBNMR, 2000. For RDC data only, -fast omits the refinement step included in examples published in Rohl&Baker, JACS, 2002. without the -fast option
  

  -skip_convergence_check <Boolean>

  this option turns off the convergence check in stage3 (score 2/5)
  

  -stage1_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage1 abinitio
  

  -stage2_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage2 abinitio
  

  -stage3a_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage3a abinitio
  

  -stage3b_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage3b abinitio
  

  -stage4_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage4 abinitio
  

  -stage5_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage5 abinitio
  

  -exit_when_converged <Boolean>

  finish abinitio if mc_converged
  Default: false
  

  -steal_3mers <Boolean>

  stealing: use 3mers from native
  Default: false
  

  -steal_9mers <Boolean>

  stealing: use 9mers from native
  Default: false
  

  -no_write_failures <Boolean>

  dont write failed structures to silent-out
  Default: false
  

  -relax_failures <Boolean>

  relax failures anyway
  Default: false
  

  -relax_with_jumps <Boolean>

  switch to allow relax even if loops are not closed
  Default: false
  

  -process_store <Boolean>

  run process_decoy on each structure in the structure store
  Default: false
  

  -fix_residues_to_native <IntegerVector>

  these residues torsions are copied from native and fixed
  Default: 0
  

  -return_full_atom <Boolean>

  return a full-atom structure even if no relax is done
  Default: false
  

  -detect_disulfide_before_relax <Boolean>

  run detect_disulfides() before relax
  Default: false
  

  -close_loops <Boolean>

  close loops
  Default: false
  

  -bGDT <Boolean>

  compute gdtmmm
  Default: true
  

  -dump_frags <Boolean>

  for control purposes... dump fragments
  Default: false
  

  -jdist_rerun <Boolean>

  go through intput structures and evaluate ( pca, rmsd, cst-energy )
  Default: false
  

  -perturb <Real>

  add some perturbation (gaussian) to phi/psi of native
  Default: 0.0
  

  -rerun <Boolean>

  go through intput structures and evaluate ( pca, rmsd, cst-energy )
  Default: false
  

  -rmsd_residues <IntegerVector>

  give start and end residue for rmsd calcul.
  Default: -1
  

  -start_native <Boolean>

  start from native structure (instead of extended)
  Default: false
  

  -debug_structures <Boolean>

  write structures to debug-out files
  Default: false
  

  -log_frags <File>

  fragment insertions (each trial) will be logged to file
  Default: ""
  

  -only_stage1 <Boolean>

  useful for benchmarks sets cycle of all higher stages to 0
  Default: false
  

  -end_bias <Real>

  set the endbias for Fragment moves
  Default: 30.0
  

  -symmetry_residue <Integer>

  hacky symmetry mode for dimers, fragments are inserted at i and i + SR - 1
  Default: -1
  

  -vdw_weight_stage1 <Real>

  vdw weight in stage1
  Default: 1.0
  

  -override_vdw_all_stages <Boolean>

  apply vdw_weight_stage1 for all stages
  Default: false
  

  -recover_low_in_stages <IntegerVector>

  say default: 2 3 4 recover_low happens in stages 2 3 4
  Default: 0
  

  -skip_stages <IntegerVector>

  say: 2 3 4, and it will skip stages 2 3 4
  Default: 0
  

  -close_chbrk <Boolean>

  Chain break closure during classic abinito
  Default: false
  

  -include_stage5 <Boolean>

  stage5 contains small moves only
  Default: false
  

  -close_loops_by_idealizing <Boolean>

  close loops by idealizing the structure after stage 4
  Default: false
  

  -optimize_cutpoints_using_kic <Boolean>

  optimize around cutpoints using kinematic relax
  Default: false
  

  -optimize_cutpoints_margin <Integer>

  
  Default: 5
  

• fold_cst

  -fold_cst <Boolean>

  fold_cst option group
  

  -constraint_skip_rate <Real>

  if e.g., 0.95 it will randomly select 5% if the constraints each round -- full-cst score in extra column
  Default: 0
  

  -violation_skip_basis <Integer>

  local skip_rate is viol/base
  Default: 100
  

  -violation_skip_ignore <Integer>

  no skip for numbers below this level
  Default: 10
  

  -keep_skipped_csts <Boolean>

  final score only with active constraints
  Default: false
  

  -no_minimize <Boolean>

  No minimization moves in fold_constraints protocol. Useful for testing wheather fragment moves alone can recapitulate a given structure.
  Default: false
  

  -force_minimize <Boolean>

  Minimization moves in fold_constraints protocol also if no constraints present
  Default: false
  

  -seq_sep_stages <RealVector>

  give vector with sequence_separation after stage1, stage3 and stage4
  Default: 0
  

  -reramp_cst_cycles <Integer>

  in stage2 do xxx cycles where atom_pair_constraint is ramped up
  Default: 0
  

  -reramp_start_cstweight <Real>

  drop cst_weight to this value and ramp to 1.0 in stage2 -- needs reramp_cst_cycles > 0
  Default: 0.01
  

  -reramp_iterations <Integer>

  do X loops of annealing cycles
  Default: 1
  

  -skip_on_noviolation_in_stage1 <Boolean>

  if constraints report no violations --- skip cycles
  Default: false
  

  -stage1_ramp_cst_cycle_factor <Real>

  spend x*<standard cycles>=""> on each step of sequence separation
  Default: 0.25
  

  -stage2_constraint_threshold <Real>

  stop runs that violate this threshold at end of stage2
  Default: 0
  

  -ignore_sequence_seperation <Boolean>

  usually constraints are switched on according to their separation in the fold-tree
  Default: false
  

  -no_recover_low_at_constraint_switch <Boolean>

  dont recover low when max_seq_sep is increased
  Default: false
  

  -ramp_coord_cst <Boolean>

  ramp coord csts just like chainbreak-weights during fold-cst
  Default: false
  

• resample

  -resample <Boolean>

  resample option group
  

  -silent <File>

  a silent file for decoys to restart sampling from
  Default: ""
  

  -tag <String>

  which decoy to select from silent file
  Default: ""
  

  -stage1 <Boolean>

  if true restart after stage1, otherwise after stage2
  Default: false
  

  -stage2 <Boolean>

  if true restart after stage1, otherwise after stage2
  Default: false
  

  -jumps <Boolean>

  if true restart after stage1, otherwise after stage2
  Default: false
  

  -min_max_start_seq_sep <RealVector>

  range of (random) start values for seq-separation
  Default: 0
  

• loopfcst

  -loopfcst <Boolean>

  loopfcst option group
  

  -coord_cst_weight <Real>

  use coord constraints for template
  Default: 0.0
  

  -coord_cst_all_atom <Boolean>

  use coord constraints on all atoms and not just CA
  Default: false
  

  -use_general_protocol <Boolean>

  use the new machinery around classes KinematicXXX
  Default: false
  

  -coord_cst_weight_array <File>

  use these weights (per seqpos) for coord cst in rigid regions
  Default: ""
  

  -dump_coord_cst_weight_array <File>

  dump these weights (per seqpos) for coord cst in rigid regions
  Default: ""
  

• jumps

  -jumps <Boolean>

  jumps option group
  

  -evaluate <Boolean>

  evaluate N-CA-C gemoetry for all jumps in the fold-tree
  Default: false
  

  -extra_frags_for_ss <File>

  use ss-def from this fragset
  Default: ""
  

  -fix_chainbreak <Boolean>

  minimize to fix ccd in re-runs
  Default: false
  

  -fix_jumps <File>

  read jump_file
  Default: ""
  

  -jump_lib <File>

  read jump_library_file for automatic jumps
  Default: ""
  

  -loop_definition_from_file <File>

  use ss-def from this file
  Default: ""
  

  -no_chainbreak_in_relax <Boolean>

  dont penalize chainbreak in relax
  Default: false
  

  -pairing_file <File>

  file with pairings
  Default: ""
  

  -random_sheets <IntegerVector>

  random sheet topology--> replaces -sheet1 -sheet2 ... select randomly up to N sheets with up to -sheet_i pairgins for sheet i
  Default: 1
  

  -residue_pair_jump_file <File>

  a file to define residue pair jump
  Default: ""
  

  -sheets <IntegerVector>

  sheet topology--> replaces -sheet1 -sheet2 ... -sheetN
  Default: 1
  

  -topology_file <File>

  read a file with topology info ( PairingStats )
  Default: ""
  

  -bb_moves <Boolean>

  Apply bb_moves ( wobble, small, shear) during stage3 and stage 4.
  Default: false
  

  -no_wobble <Boolean>

  Don t apply the useless wobble during stage3 and stage 4.
  Default: false
  

  -no_shear <Boolean>

  Don t apply the useless shear during stage3 and stage 4.
  Default: false
  

  -no_sample_ss_jumps <Boolean>

  sample jump-frags during folding
  Default: false
  

  -invrate_jump_move <Integer>

  give 5 here to have 5 torsion moves for each jump move
  Default: 10
  

  -chainbreak_weight_stage1 <Real>

  the weight on chainbreaks
  Default: 1.0
  

  -chainbreak_weight_stage2 <Real>

  the weight on chainbreaks
  Default: 1.0
  

  -chainbreak_weight_stage3 <Real>

  the weight on chainbreaks
  Default: 1.0
  

  -chainbreak_weight_stage4 <Real>

  the weight on chainbreaks
  Default: 1.0
  

  -ramp_chainbreaks <Boolean>

  ramp up the chainbreak weight stage1-0, stage2 0.25, stage3 alternating 0.5..2.5, stage4 2.5..4
  Default: true
  

  -increase_chainbreak <Real>

  multiply ramped chainbreak weight by this amount
  Default: 1.0
  

  -overlap_chainbreak <Boolean>

  use the overlap chainbrak term in stage4
  Default: false
  

  -sep_switch_accelerate <Real>

  constraints and chainbreak depend on in-chain-separation. Accelerate their enforcement 1+num_cuts()*<this_factor>
  Default: 0.4
  

  -dump_frags <Boolean>

  dump jump_fragments
  Default: false
  

  -njumps <Integer>

  number_of_jumps to select from library for each trajectory (membrane mode)
  Default: 1
  

  -max_strand_gap_allowed <Integer>

  merge strands if they less than X residues but same register
  Default: 2
  

  -contact_score <Real>

  the strand-weight will have a weight * contact_order component
  Default: 0.0
  

• templates

  -templates <Boolean>

  templates option group
  

  -config <File>

  read a list of templates and alignments
  Default: "templates.dat"
  

  -fix_aligned_residues <Boolean>

  pick only from template fragments and then keep these residues fixed
  Default: false
  

  -fix_frag_file <File>

  fragments from this file are picked once in beginning and then kept fixed
  Default: ""
  

  -fix_margin <Integer>

  keep n residues at edges of fixed fragments moveable
  Default: 1
  

  -min_nr_large_frags <Integer>

  how many large fragments should be present
  Default: 100000
  

  -min_nr_small_frags <Integer>

  how many small fragments should be present
  Default: 100000
  

  -no_pick_fragments <Boolean>

  no further fragment picking from templates
  Default: false
  

  -nr_large_copies <Integer>

  make N copies of each picked template fragment -- a hacky way to weight them
  Default: 4
  

  -nr_small_copies <Integer>

  make N copies of each picked template fragment -- a hacky way to weight them
  Default: 20
  

  -pairings <Boolean>

  use pairings from templates
  Default: false
  

  -pick_multiple_sizes <Boolean>

  pick 9mers, 18mers and 27mers
  Default: false
  

  -strand_constraint <Boolean>

  use the template-based strand-constraints
  Default: false
  

  -vary_frag_size <Boolean>

  pick fragments as long as aligned regions
  Default: false
  

  -no_culling <Boolean>

  dont throw out constraints that are violated by other templates
  Default: false
  

  -helix_pairings <File>

  file with list of pairings that are enforced (pick jumps from templates with H)
  Default: ""
  

  -prefix <File>

  path for config directory -- applied to all filenames in template_config_file
  Default: ""
  

  -change_movemap <Integer>

  stage in which movemap is switched to allow all bb-residues to move, valid stages: 3..4 (HACK)
  Default: 3
  

  -force_native_topology <Boolean>

  force the native toplogy (geometries from templates)
  Default: false
  

  -topology_rank_cutoff <Real>

  select jumps from all topologies with a higher relative score than if 1.0 take top 5
  Default: 1.0
  

  -min_frag_size <Integer>

  smallest fragment picked from aligned template regions
  Default: 6
  

  -max_shrink <Integer>

  pick fragments up to max_shrink smaller than aligned regions
  Default: 0
  

  -shrink_step <Integer>

  shrink_step 5 , eg., 27mer 22mer 17mer
  Default: 5
  

  -shrink_pos_step <Integer>

  distance between start pos in shrinked fragments
  Default: 5
  

  -min_padding <Integer>

  minimum space between fragment and gap
  Default: 0
  

  -min_align_pos <Integer>

  ignore aligned residues before this position
  Default: 0
  

  -max_align_pos <Integer>

  ignore aligned residues after this position
  Default: -1
  

• templates:cst

  -cst <Boolean>

  cst option group
  

  -topN <Integer>

  topN ranking models are used for constraints ( culling and source )
  Default: 0
  

  -wTopol <Real>

  weight for beta-pairing topology score in ranking
  Default: 0.5
  

  -wExtern <Real>

  weight for external score ( column in template_config_file, e.g, svn-score
  Default: 0.5
  

• templates:fragsteal

  -fragsteal <Boolean>

  fragsteal option group
  

  -topN <Integer>

  topN ranking models are used for fragment stealing
  Default: 0
  

  -wTopol <Real>

  weight for beta-pairing topology score in ranking
  Default: 0.5
  

  -wExtern <Real>

  weight for external score ( column in template_config_file, e.g, svn-score
  Default: 0.5
  

• abrelax

  -abrelax <Boolean>

  ab initio relax mode
  

  -filters <Boolean>

  
  

  -fail_unclosed <Boolean>

  structures which don't close loops are reported as FAIL_DO_NOT_RETRY
  Default: false
  

• score

  -score <Boolean>

  scorefunction option group
  

  -weights <String>

  Name of weights file (without extension .wts)
  Default: "standard"
  

  -custom_atom_pair <String>

  filename for custom atom pair constraints
  Default: "empty"
  

  -patch <String>

  Name of patch file (without extension)
  Default: ""
  

  -empty <Boolean>

  Make an empty score - i.e. NO scoring
  

  -fa_max_dis <Real>

  How far does the FA pair potential go out to ?
  Default: 6.0
  

  -fa_Hatr <Boolean>

  Turn on Lennard Jones attractive term for hydrogen atoms
  

  -no_smooth_etables <Boolean>

  Revert to old style etables
  

  -etable_lr <Real>

  lowers energy well at 6.5A
  

  -input_etables <String>

  Read etables from files with given prefix
  

  -output_etables <String>

  Write out etables to files with given prefix
  

  -rms_target <Real>

  Target of RMS optimization for RMS_Energy EnergyMethod
  Default: 0.0
  

  -ramaneighbors <Boolean>

  Uses neighbor-dependent ramachandran maps
  Default: false
  

  -optH_weights <String>

  Name of weights file (without extension .wts) to use during optH
  

  -optH_patch <String>

  Name of weights file (without extension .wts) to use during optH
  

  -hbond_params <String>

  Directory name in the database for which hydrogen bond parameters to use.
  Default: "standard_params"
  

  -symE_units <Integer>

  Number of symmetric Units in design for use with symE scoring
  Default: -1
  

  -symE_bonus <Real>

  Energy bonus per match for use with symE scoring
  Default: 0.0
  

  -NV_lbound <Real>

  Lower Bound for neighbor Vector scoring
  Default: 3.3
  

  -NV_ubound <Real>

  Upper Bound for neighbor Vector scoring
  Default: 11.1
  

  -NV_table <String>

  Location of path to potential lookup table
  Default: "neighbor_vector_score.histogram"
  

  -disable_orientation_dependent_rna_ch_o_bonds <Boolean>

  Do not use orientation-dependent potential for RNA carbon hydrogen bonds
  Default: false
  

  -find_neighbors_3dgrid <Boolean>

  Use a 3D lookup table for doing neighbor calculations. For spherical, well-distributed conformations, O(N) neighbor detection instead of general O(NlgN)
  Default: false
  

  -seqdep_refene_fname <String>

  Filename for table containing sequence-dependent reference energies
  

  -secondary_seqdep_refene_fname <String>

  Additional filename for table containing sequence-dependent reference energies
  

  -exact_occ_pairwise <Boolean>

  When using occ_sol_exact, compute energies subject to pairwise additivity (not recommended - intended for parameterization / evaluation purposes)
  Default: false
  

  -exact_occ_skip_Hbonders <Boolean>

  When using occ_sol_exact, do not count contributions from occluding groups which form Hbonds to the polar group of interest
  Default: true
  

  -exact_occ_include_Hbond_contribution <Boolean>

  When using occ_sol_exact, include Hbonds in the solvation energy
  Default: false
  

  -exact_occ_pairwise_by_res <Boolean>

  When using occ_sol_exact, compute energies subject to by-residue pairwise additivity (not recommended - intended for parameterization / evaluation purposes)
  Default: false
  

  -exact_occ_split_between_res <Boolean>

  When using occ_sol_exact with the exact_occ_pairwise flag, split the energies between both contributing residues instead of assigning it just to the polar residue (not recommended - intended for parameterization / evaluation purposes)
  Default: false
  

  -exact_occ_self_res_no_occ <Boolean>

  Setting this to false means that the self-residue CAN occlude when using the exact ODO model, leading to potential double-counting with the Dunbrack energy but better results in loop discrimination.
  Default: false
  

  -exact_occ_radius_scaling <Real>

  When using occ_sol_exact, scale the radii of occluding atoms by this factor (intended for parameterization / evaluation purposes)
  Default: 1.0
  

  -ref_offsets <StringVector>

  offset reference energies using 3 character residue types (example: TRP 0.9 HIS 0.3)
  

  -output_residue_energies <Boolean>

  Output the energy for each residue
  Default: false
  

  -fa_custom_pair_distance_file <String>

  Name of custom pair distance energy file
  Default: ""
  

  -disulf_matching_probe <Real>

  Size of probe to use in disulfide matching score
  Default: 2.5
  

• score:saxs

  -saxs <Boolean>

  saxs option group
  

  -custom_ff <String>

  Name of config file providing extra from factors
  Default: ""
  

  -ref_fa_spectrum <File>

  reads reference full-atom spectrum from a file
  

  -ref_cen_spectrum <File>

  reads reference centroid spectrum from a file
  

  -ref_spectrum <File>

  reads reference spectrum from a file
  

  -ref_pddf <File>

  reads reference pairwise distance distribution function
  

  -skip_hydrogens <Boolean>

  skip hydrogen atoms
  Default: false
  

  -d_min <Real>

  minimum value of distance used in PDDF score evaluation (in [A])
  Default: 5.0
  

  -d_max <Real>

  maximum value of distance used in PDDF score evaluation (in [A])
  Default: 100.0
  

  -d_step <Real>

  step of distance used in PDDF score evaluation (in [A])
  Default: 0.1
  

  -q_min <Real>

  minimum value of q used in spectra calculations (in [A^-1])
  Default: 0.01
  

  -q_max <Real>

  maximum value of q used in spectra calculations (in [A^-1])
  Default: 0.25
  

  -q_step <Real>

  step of q used in spectra calculations (in [A^-1])
  Default: 0.01
  

  -fit_pddf_area <Boolean>

  PDDF curve for a scored pose will be normalized to match the area under the reference PDDF curve
  Default: false
  

• score

  -sidechain_buried <IntegerVector>

  count buried residues (rvernon pilot app)
  Default: -1
  

  -sidechain_exposed <IntegerVector>

  count exposed residues (rvernon pilot app)
  Default: -1
  

• corrections

  -corrections <Boolean>

  corrections option group
  

  -correct <Boolean>

  turn on default corrections:-corrections::chemical:icoor_05_2009-corrections::score:no_his_his_pairE-scoring::hbond_params helix_hb_06_2009-corrections::score:hbond_fade 1.9 2.3 2.3 2.6 0.3 0.7 0.0 0.05-corrections::score:ch_o_bond_potential ch_o_bond_potential_near_min_yf.dat
  Default: false
  

• corrections:score

  -score <Boolean>

  score option group
  

  -no_his_his_pairE <Boolean>

  Set pair term for His-His to zero
  

  -hbond_His_Phil_fix <Boolean>

  Phil's fix on Histidine interaction angular dependence
  

  -helix_hb_06_2009 <Boolean>

  Helix backbone-backbone hbond potential with a different angular dependence
  

  -p_aa_pp <String>

  Name of P_AA_PP potential file (search in the local directory first, then look in the database)
  Default: "P_AA_pp"
  

  -p_aa_pp_nogridshift <Boolean>

  the format of p_aa_pp changed from using i*10+5 (5, 15, etc) to i*10 (0,10,etc.) as grid points
  

  -rama_not_squared <Boolean>

  Rama potential calculated as input for both rama and rama2b. By default, the potential is square for (rama+entropy) > 1.0
  

  -rama_map <File>

  Ramachandran file used by rama
  Default: "Rama_smooth_dyn.dat_ss_6.4"
  

  -dun08 <Boolean>

  Use the 2008 Dunbrack library instead of the 2002 library.
  

  -dun08_dir <String>

  Name of dun08 dir
  Default: "dun08"
  

  -ch_o_bond_potential <String>

  Name of ch_o_bond potential file (search in the local directory first, then look in the database)
  Default: "ch_o_bond_potential.dat"
  

  -hack_elec_co_only <Boolean>

  Using only CO-CO interactions in hack_elec_bb_bb
  Default: false
  

  -hbond_no_lr <Boolean>

  Disable the long-range part of angular dependent potential. It does not affect the distance dependent part of the potential
  Default: false
  

  -hbond_fade <RealVector>

  User defined fading paramters for hbond, a vector of eight numbers. first four are lower distance cutoff, lower distance ramping, upper distance ramping, upper distance cutoff; next two are lower -cos(theta) cutoff and ramping (angle at proton donor), and the last two are lower -cos(psi) cutoff and ramping (angle at acceptor). default value in the code is 1.9 2.3 2.3 3.0 0.0 0.05 0.0 0.05
  Default: utility::vector1<float>(8,-1)
  

  -lj_hbond_hdis <Real>

  Lennard Jones sigma value for hatms, classically it's been at 1.95 but the average A-H distance for hydrogen bonding is 1.75 from crystal structures. (momeara)
  Default: 1.95
  

  -lj_hbond_OH_donor_dis <Real>

  Lennard Jones sigma value for O in OH donor groups. Classically it has been 3.0 but the average distances from crystal structurs is 2.6 (momeara)
  Default: 3.0
  

• corrections:chemical

  -chemical <Boolean>

  chemical option group
  

  -icoor_05_2009 <Boolean>

  New set of idealized coordinates for full atom, 05-2009
  

• holes

  -holes <Boolean>

  holes option group
  

  -dalphaball <File>

  The DAlaphaBall_surf program
  

  -params <File>

  File containing score parameters
  Default: "holes_params.dat"
  

  -h_mode <Integer>

  include H's or no... see PoseBalls.cc
  Default: 0
  

  -water <Boolean>

  include water or no
  Default: false
  

  -make_pdb <Boolean>

  make pdb with scores
  Default: false
  

  -make_voids <Boolean>

  do separate SLOW void calculation
  Default: false
  

  -atom_scores <Boolean>

  output scores for all atoms
  Default: false
  

  -residue_scores <Boolean>

  output scores for all residues (avg over atoms)
  Default: false
  

  -cav_shrink <Real>

  Cavity ball radii reduced by this amount
  Default: 0.7
  

  -minimize <String>

  RosettaHoles params to use: decoy15, decoy25 or resl
  Default: "decoy15"
  

• packstat

  -packstat <Boolean>

  packstat option group
  

  -include_water <Boolean>

  Revert to old style etables
  Default: false
  

  -oversample <Integer>

  Precision of SASA measurements
  Default: 0
  

  -packstat_pdb <Boolean>

  Output a pdb with packing visualizations
  Default: false
  

  -surface_accessibility <Boolean>

  Compute extra cavity burial information
  Default: false
  

  -residue_scores <Boolean>

  Output the score for each resdiue
  Default: false
  

  -cavity_burial_probe_radius <Real>

  Radius probe to consider a cavity buried
  Default: 1.4
  

  -raw_stats <Boolean>

  Output the raw stats per-residue (for training, etc...)
  Default: false
  

  -threads <Integer>

  Number of threads to use (0 for no threading)
  Default: 0
  

  -cluster_min_volume <Real>

  voids smaller than this will not be shown.
  Default: 30
  

  -min_surface_accessibility <Real>

  voids must be at least this exposed
  Default: -1.0
  

  -min_cluster_overlap <Real>

  void-balls must overlap by this much to be clustered
  Default: 0.1
  

  -min_cav_ball_radius <Real>

  radius of smallest void-ball to consider
  Default: 0.7
  

  -max_cav_ball_radius <Real>

  radius of largest void-ball to consider
  Default: 3.0
  

• crossmatch

  -crossmatch <Boolean>

  crossmatch option group
  

  -write_reduced_matchset <StringVector>

  <name> <pdb1> <pdb2> ...
  

  -interface_size <Integer>

  num CB-CB within 8A
  Default: 30
  

  -max_dis_any <Real>

  
  Default: 3.0
  

  -max_dis_all <Real>

  
  Default: 2.6
  

  -max_dis_metal <Real>

  
  Default: 1.0
  

  -clash_dis <Real>

  
  Default: 3.0
  

  -identical_match_dis <Real>

  
  Default: 0.0001
  

• smhybrid

  -smhybrid <Boolean>

  smhybrid option group
  

  -add_cavities <Boolean>

  output cavities in result pdbs
  Default: false
  

  -abinitio_design <Boolean>

  do a design run in centroid mode
  Default: true
  

  -fa_refine <Boolean>

  Do nobu's flxbb
  Default: true
  

  -virtual_nterm <Boolean>

  remove Nterm
  Default: false
  

  -debug <Boolean>

  debug
  Default: false
  

  -refine <Boolean>

  don't do bit centroid moves
  Default: false
  

  -filter <Boolean>

  filter centroid results as you go
  Default: false
  

  -floating_scs_rep <Boolean>

  should floating scs repel those in other subunits?
  Default: false
  

  -flxbb <Boolean>

  allow bb moves in minimization
  Default: false
  

  -centroid_all_val <Boolean>

  mutate all to VAL in centroid mode
  Default: false
  

  -subsubs_attract <Boolean>

  attract subsubs togeher
  Default: false
  

  -linker_cst <Boolean>

  attract N/C termini for linker
  Default: false
  

  -pseudosym <Boolean>

  HACK pseudosymmetry
  Default: false
  

  -design_linker <Boolean>

  allow design on added 'linker' residues
  Default: true
  

  -design <Boolean>

  allow design on added 'linker' residues
  Default: true
  

  -restrict_design_to_interface <Boolean>

  allow design on added 'linker' residues
  Default: false
  

  -restrict_design_to_subsub_interface <Boolean>

  allow design on added 'linker' residues
  Default: false
  

  -design_hydrophobic <Boolean>

  design all hydrophobic
  Default: false
  

  -add_metal_at_0 <Boolean>

  DEPRECATED
  Default: false
  

  -nres_mono <Integer>

  target number of residues per monomer
  Default: 20
  

  -abinitio_cycles <Integer>

  number of abinitio cycles
  Default: 10000
  

  -primary_subsubunit <Integer>

  primary subunut
  Default: 1
  

  -minbb <Integer>

  level of bb min 0=None 1=little 2=all
  Default: 1
  

  -switch_concert_sub <Integer>

  assume prmary subsub is on this subunit for concerted RB moves
  Default: 1
  

  -temperature <Real>

  MC temp for cen fold
  Default: 2.0
  

  -inter_subsub_cst <Boolean>

  add dis csts inter-subsub
  Default: false
  

  -rb_mag <Real>

  magnitude of rb moves
  Default: 1.0
  

  -ss <String>

  secondary structure
  Default: ""
  

  -symm_def_template <File>

  template for symmetry definition file
  

  -symm_def_template_reduced <File>

  template for reduced symmetry definition file
  

  -attach_as_sc <IntegerVector>

  attach the group via side chain
  

  -attach_as_sc_sub <IntegerVector>

  attach the group via side chain in this sub
  

  -inversion_subs <IntegerVector>

  subunits to be inverted, if any
  

  -chainbreaks <BooleanVector>

  close chainbreak from this subsub to the next
  

  -design_res_files <StringVector>

  files containing designable residues for each component pose
  Default: ""
  

  -fixed_res_files <StringVector>

  files containing fixed residues (no repack even) for each component pose
  Default: ""
  

  -frag_res_files <StringVector>

  files containing residues ok to insert frags into. will have starting ss
  Default: ""
  

  -scattach_res_files <StringVector>

  files containing residues ok to scattach to.
  Default: ""
  

  -rep_edge_files <StringVector>

  files containing residues which are edge strands.
  Default: ""
  

  -virtual_res_files <StringVector>

  files containing residues that should be virtual
  Default: ""
  

  -jumpcut_files <StringVector>

  file specifying jumps and cuts for subsubunits
  Default: ""
  

  -cst_sub_files <StringVector>

  file specifying which subunits are part of a structural unit and shoudl be constrained
  Default: ""
  

  -symm_file_tag <StringVector>

  label for each subunit
  Default: ""
  

  -attach_atom <StringVector>

  attach atom on each subunit
  Default: ""
  

  -add_res_before <StringVector>

  SS to add before each subunit region
  Default: ""
  

  -add_res_after <StringVector>

  SS to add after each subunit region
  Default: ""
  

  -add_ss_before <StringVector>

  residues to add
  Default: ""
  

  -add_ss_after <StringVector>

  SS to add after each subunit region
  Default: ""
  

  -add_atom_at_cen <StringVector>

  SS to add after each subunit region
  Default: ""
  

  -attach_rsd <StringVector>

  attach rsd on each subunit
  Default: ""
  

• evolution

  -evolution <Boolean>

  evolution option group
  

  -parentlist <FileVector>

  File(s) containing list(s) of Parent PDB files to process
  

  -childlist <FileVector>

  File(s) containing list(s) of Parent PDB files to process
  

  -action <String>

  One of the following: diversify, intensify
  Default: "diversify"
  

  -rms_threshold <Real>

  RMS Clustering threshold
  Default: 3.5
  

  -rms_topmargin <Real>

  RMS Clustering threshold
  Default: 5.0
  

  -targetdir <String>

  Write target new parent polulation to this directory !
  Default: "./"
  

  -padding_score_filter <Real>

  RMS Clustering threshold
  Default: 5.0
  

  -padding_stage2_filter <Real>

  RMS Clustering threshold
  Default: 15.0
  

• cluster

  -cluster <Boolean>

  cluster option group
  

  -input_score_filter <Real>

  Only read in structures below a certain energy
  Default: 1000000.0
  

  -output_score_filter <Real>

  Only read in structures below a certain energy
  Default: 1000000.0
  

  -exclude_res <IntegerVector>

  Residue numbers to be excluded from cluster RMS calculation
  Default: -1
  

  -thinout_factor <Real>

  Ignore this fraction of decoys in the first round !
  Default: -1
  

  -max_cluster_seeds <Integer>

  Do not calculate initial cluster centers for more then this many structuers
  Default: 500
  

  -radius <Real>

  Cluster radius
  Default: 3.0
  

  -limit_cluster_size <Integer>

  For each cluster only retain top N
  Default: -1
  

  -limit_clusters <Integer>

  Only retain largest N clusters
  Default: 100
  

  -limit_total_structures <Integer>

  Only retain the first N structures (ordered by cluster number)
  Default: -1
  

  -max_total_cluster <Integer>

  Only ever make N clusters or less
  Default: 1000
  

  -gdtmm <Boolean>

  Cluster by gdtmm instead of RMS
  Default: false
  

  -sort_groups_by_energy <Boolean>

  Sort clusters by energy
  Default: false
  

  -remove_singletons <Boolean>

  Get rid of single-member clusters
  Default: false
  

  -export_only_low <Boolean>

  Print only the lowest energy member
  Default: false
  

  -remove_highest_energy_member <Boolean>

  Remove highest energy member from each cluster
  Default: false
  

  -idealize_final_structures <Boolean>

  Run an idealization over the resulting structures
  Default: false
  

  -limit_dist_matrix <Integer>

  Only calculate full matrix for a subset of structres. Then simply assign structures to nearest cluster
  Default: -1
  

  -make_ensemble_cst <Boolean>

  Create a set of constraints describing the variablity in each cluster of each residue.
  Default: false
  

  -hotspot_hash <Boolean>

  Cluster hotspot hashing results. Each input PDB must contain both the target and the newly docked hotspot (which should be the last residue in the pose).
  Default: false
  

  -loops <Boolean>

  Cluster this loop
  Default: false
  

  -population_weight <Real>

  Order Clusters by (1-p)*score - p*size whpere p = population_weight
  Default: 0.09
  

  -template_scores <String>

  imple textfile containing template names (in caps) and scores.
  

  -K_level <Integer>

  Hierarchical cluster level number
  Default: 1
  

  -K_radius <RealVector>

  Radius list of different level of cluster
  Default: utility::vector1<float>(1, 2.0)
  

  -K_n_cluster <IntegerVector>

  How many clusters in each level
  Default: utility::vector1<int>(1, 10000)
  

  -K_style <StringVector>

  Which K-cluster engine to use
  Default: utility::vector1<std::string>(9, "GKC")
  

  -K_threshold <Real>

  Threshold for test the convergence of iteration
  Default: 0.01
  

  -K_n_sub <Integer>

  Number of clusters in subdir
  Default: 100
  

  -K_deque_size <Integer>

  Size of subcluster deque
  Default: 20
  

  -K_deque_level <Integer>

  Provide deque in top level
  Default: 1
  

  -K_redundant <Boolean>

  Keep all the higher level center structure in sub-pools
  Default: true
  

  -K_not_fit_xyz <Boolean>

  Do not rotate xyz when calculate rmsd
  Default: false
  

  -K_save_headers <Boolean>

  Save headers in silent file
  Default: false
  

• rescore

  -rescore <Boolean>

  rescore option group
  

  -pose_metrics <Boolean>

  Do pose metrics calc
  

  -skip <Boolean>

  Dont actually call scoring function (i.e. get evaluators only)
  

  -verbose <Boolean>

  Full break down of weights, raw scores and weighted scores ?
  

  -msms_analysis <String>

  Run MSMS on the structure and determine surface properties.
  

• mc

  -mc <Boolean>

  mc option group
  

  -hierarchical_pool <String>

  specify prefix in order to look for hierarchical pool
  

  -read_structures_into_pool <File>

  specify the silent-structs to create a hierarchy for lazy users
  

  -convergence_check_frequency <Integer>

  how often check for convergences in MC object?
  Default: 100
  

  -known_structures <File>

  specify a filename of a silent-file containing known structures
  Default: "known_structs.in"
  

  -max_rmsd_against_known_structures <Real>

  stop sampling if rmsd to a known-structure is lower than X
  Default: 1.5
  

  -heat_convergence_check <Integer>

  jump out of current abinitio run if X unsuccesful mc-trials reached
  Default: 0
  

• batch_relax

  -batch_relax <Boolean>

  batch_relax option group
  

  -batch_size <Integer>

  Size of batches - note that thsie affects memory usage significantly
  Default: 100
  

• relax

  -relax <Boolean>

  relax option group
  

  -fast <Boolean>

  Do a preset, small cycle number FastRelax
  

  -thorough <Boolean>

  Do a preset, large cycle number FastRelax
  

  -membrane <Boolean>

  Do membrane relax
  Default: false
  

  -default_repeats <Integer>

  Default number of repeats done by FastRelax. Has no effect if a custom script is used!
  Default: 5
  

  -ramady <Boolean>

  Run ramady code which aleviates stuck bad ramachandran energies
  Default: false
  

  -script <File>

  Relax script file
  Default: ""
  

  -script_max_accept <Integer>

  Limit number of best accepts
  Default: 10000000
  

  -superimpose_to_native <Boolean>

  Superimpose input structure to native
  Default: false
  

  -constrain_relax_to_native_coords <Boolean>

  For relax and fastrelax, tether backbone coordinates of the pdbs being relaxed to the coordinates in the xtal native
  Default: false
  

  -constrain_relax_to_start_coords <Boolean>

  For relax and fastrelax, tether backbone coordinates of the pdbs being relaxed to the coordinates in the xtal native
  Default: false
  

  -bb_move <Boolean>

  allow backbone to move during relax
  Default: true
  

  -chi_move <Boolean>

  allow sidechain to move during relax
  Default: true
  

  -jump_move <Boolean>

  allow jump to move during relax
  Default: false
  

  -minimize_bond_lengths <Boolean>

  Free bond length DOFs during relax for all atoms
  Default: false
  

  -minimize_bond_angles <Boolean>

  Free bond angle DOFs during relax for all atoms
  Default: false
  

  -minimize_mainchain_bond_lengths <Boolean>

  Free bond length DOFs for mainchain heavy atoms
  Default: false
  

  -minimize_mainchain_bond_angles <Boolean>

  Free bond angle DOFs for mainchain heavy atoms
  Default: false
  

  -chainbreak_weight <Real>

  chainbreak weight
  Default: 0.0
  

  -linear_chainbreak_weight <Real>

  linear chainbreak weight
  Default: 0.0
  

  -overlap_chainbreak_weight <Real>

  overlap chainbreak weight
  Default: 0.0
  

  -classic <Boolean>

  Do very old classic relax ! This is a poor protocol - don't use it !
  

  -sequence_file <File>

  Relax script file
  Default: ""
  

  -quick <Boolean>

  Do a preset, small cycle number FastRelax
  

  -sequence <Boolean>

  Do a preset, small cycle number FastRelax
  

  -minirelax_repeats <Integer>

  
  Default: 2
  

  -minirelax_sdev <Real>

  tether on coordinate constraints for minirelax
  Default: 0.5
  

  -wobblemoves <Boolean>

  Do Wobble moves ?
  Default: false
  

  -constrain_relax_segments <File>

  loop definition file
  Default: ""
  

  -coord_cst_width <Real>

  Width on coordinate constraints from constrain_relax_* options
  Default: 0.0
  

  -coord_cst_stdev <Real>

  Stdev on coordinate constraints from constrain_relax_* options
  Default: 0.5
  

  -ramp_constraints <Boolean>

  Ramp constraints during phase1 of relax from full to zero
  Default: false
  

  -energycut <Real>

  Rottrial energycut (per residue!)
  Default: 0.01
  

  -mini <Boolean>

  perform a relax that is only a minimization and repack.
  Default: false
  

  -stage1_ramp_cycles <Integer>

  Ramp cyclesin stage 1
  Default: 8
  

  -stage1_ramp_inner_cycles <Integer>

  Inner cycles means how many small shear moves + rottrials
  Default: 1
  

  -stage2_repack_period <Integer>

  Full repack after how many cycles in stage 2
  Default: 100
  

  -stage2_cycles <Integer>

  How many stage 2 cycles ? (by default its -1 means Nresidues*4 )
  Default: -1
  

  -min_tolerance <Real>

  Minimizer tolerance
  Default: 0.00025
  

  -stage3_cycles <Integer>

  How many stage 3 cycles ? (by default its -1 means Nresidues )
  Default: -1
  

  -cycle_ratio <Real>

  Post-multiplier for cycle numbers
  Default: 1.0
  

  -filter_stage2_beginning <Real>

  FArelax score filter
  Default: 99999999.00
  

  -filter_stage2_quarter <Real>

  FArelax score filter
  Default: 99999999.00
  

  -filter_stage2_half <Real>

  FArelax score filter
  Default: 99999999.00
  

  -filter_stage2_end <Real>

  FArelax score filter
  Default: 99999999.00
  

• enzdes

  -enzdes <Boolean>

  enzdes option group
  

  -checkpoint <String>

  write/read checkpoint files to the desired filename.
  Default: ""
  

  -enz_score <Boolean>

  prevent repacking in enzyme design calculation
  Default: false
  

  -enz_repack <Boolean>

  prevent redesign in enzyme design calculation
  Default: false
  

  -cst_opt <Boolean>

  pre design constraint minimization
  Default: false
  

  -cst_predock <Boolean>

  docks a ligand relative the catalytic residue
  Default: false
  

  -trans_magnitude <Real>

  rigid body translation in Angstrom
  Default: 0.1
  

  -rot_magnitude <Real>

  rigid body rotation in deg
  Default: 2
  

  -dock_trials <Real>

  number of docking trials
  Default: 100
  

  -cst_min <Boolean>

  after design minimization, constraints turned off
  Default: false
  

  -cst_design <Boolean>

  invokes actual design
  Default: false
  

  -design_min_cycles <Integer>

  determines how many iterations of designing/minimizing are done during a design run
  Default: 1
  

  -bb_min <Boolean>

  allows backbone of active site residues to move during cst_opt and cst_min. In the cst_opt stage, residue Cas will be constrained to their original positions.
  Default: false
  

  -bb_min_allowed_dev <Real>

  distance by which Cas are allowed to move during backbone minimization before a penalty is assigned.
  Default: 0.5
  

  -loop_bb_min_allowed_dev <Real>

  distance by which Cas are allowed to move during backbone minimization before a penalty is assigned. Applied only for loops as determined by DSSP.
  Default: 0.5
  

  -minimize_ligand_torsions <Real>

  degrees by which ligand torsions are allowed to rotate before a penalty is assigned. Only those torsions which have diversity in the conformational ensemble are allowed this std dev. rest are constrained to 0.1
  Default: 10.0
  

  -minimize_all_ligand_torsions <Real>

  allows constrained minimization of all ligand torsions using stddev.
  Default: 10.0
  

  -chi_min <Boolean>

  allows chi values of active site residues to move during cst_opt and cst_min.
  Default: false
  

  -min_all_jumps <Boolean>

  allows all jumps in the pose to minimize during cst_opt and cst_min. By default only ligand-associated jumps minimize
  Default: false
  

  -cst_dock <Boolean>

  ligand docking after design. By default, constraints (except covalent connections will be turned off for this stage.
  Default: false
  

  -enz_debug <Boolean>

  invokes various debug routines around the enzdes code
  Default: false
  

  -cstfile <File>

  file that contains all necessary constraints for an enzyme design calculation
  Default: "constraints.cst"
  

  -enz_loops_file <File>

  file that contains definitions of loop regions
  Default: "eloops.els"
  

  -flexbb_protocol <Boolean>

  triggers flexible backbone design
  Default: false
  

  -remodel_protocol <Boolean>

  triggers remodel protocol design
  Default: false
  

  -kic_loop_sampling <Boolean>

  Generate alternate loop conformations using KIC loop closure instead of backrub
  Default: false
  

  -dump_loop_samples <String>

  yes/no? Create loop pdb files named loopreg_[regionid]_[whichsample].pdb for the chosen loop samples; if 'quit_afterwards' is given, then the program exits after all loops have been generated
  Default: "no"
  

  -fix_catalytic_aa <Boolean>

  preventing catalytic aa from repacking
  Default: false
  

  -additional_packing_ligand_rb_confs <Integer>

  Ligand Rotamers will be built at additional random rigid body positions during packing
  Default: 0
  

  -ex_catalytic_rot <Integer>

  convenience option to use higher number of rotamers for catalytic residues. The chosen level will be applied to all chis of every catalytic residue.
  Default: 1
  

  -single_loop_ensemble_size <Integer>

  number of conformations generated for each of the independent loops in a flexbb calculation
  Default: 100
  

  -loop_generator_trials <Integer>

  number of trials of that the respective loop generator(backrub/kinematic kic) does in enzdes flexbb
  Default: 200
  

  -no_catres_min_in_loopgen <Boolean>

  prevents minimization of catalytic residues when generating loop ensembles
  Default: false
  

  -mc_kt_low <Real>

  low monte carlo limit for ensemble generation using backrub
  Default: 0.6
  

  -mc_kt_high <Real>

  high monte carlo limit for ensemble generation using backrub
  Default: 0.9
  

  -min_cacb_deviation <Real>

  Fragment uniqueness filter. On by default. Minimum CA/CB average deviation that at least one residue must have from all other already-included fragments for a new fragment to be included
  Default: 0.3
  

  -max_bb_deviation <Real>

  Fragment smoothness filter. Off by default. Upper limit on the backbone average deviation a new fragment may have to its most-similar fragment that has already been included in the fragment set.
  Default: 0.1
  

  -max_bb_deviation_from_startstruct <Real>

  Fragment native-proximity Filter. Always on. Maximum tolerated backbone average deviation from the starting backbone for a fragment that to be included in the fragment set.
  Default: 1.5
  

  -flexbb_outstructs <Integer>

  doesn't do much anymore in the current implementation of the flexbb protocol
  Default: 10
  

  -remodel_trials <Integer>

  how often each loop is being remodeled in the enzdes_remodel mover
  Default: 100
  

  -remodel_secmatch <Boolean>

  if constrained interactions are missing in the pose during remodel, the SecondaryMatcher will be used to try to find them in the remodeled region. very experimental at this point
  Default: false
  

  -dump_inverse_rotamers <Boolean>

  in case of remodel secmatching against inverse rotamers, these rotamers will be dumped before the protocol starts for visual inspection by the user
  Default: false
  

  -remodel_aggressiveness <Real>

  determines the aggressiveness with which a given loop is remodeled. legal values between 0 and 1, where 1 is aggressive and 0 conservative.
  Default: 0.1
  

  -favor_native_res <Real>

  a bonus energy assigned to the native res during a design calculation
  Default: 0.5
  

  -detect_design_interface <Boolean>

  automatically detect design/repack region around ligand(s)
  Default: false
  

  -include_catres_in_interface_detection <Boolean>

  if option -detect_design_interface is active, invoking this option causes all residues that are within the specified cuts of any catalytic residue are also set to designing/repacking
  Default: false
  

  -cut1 <Real>

  option to specify redesign cutoff 1 in enzdes calculation
  Default: 0.0
  

  -cut2 <Real>

  option to specify redesign cutoff 2 in enzdes calculation
  Default: 0.0
  

  -cut3 <Real>

  option to specify repack cutoff 1 in enzdes calculation
  Default: 10.0
  

  -cut4 <Real>

  option to specify repack cutoff 2 in enzdes calculation
  Default: 10.0
  

  -lig_packer_weight <Real>

  specifies the weights for protein ligand interaction during packing (and only packing!! )
  Default: 1.0
  

  -no_unconstrained_repack <Boolean>

  no unconstrained repacking after the design stage
  Default: false
  

  -secmatch_Ecutoff <Real>

  the maximum constraint energy at which a residue is accepted in the secondary matcher
  Default: 1.0
  

  -change_lig <File>

  Can be used with the secondary matching protocol if different incarnations of the ligand are used for design and primary matching. The file needs to contain information on what atoms to superimpose.
  Default: "ligchange_file.txt"
  

  -process_ligrot_separately <String>

  In the EnzdesFixBB protocol, causes the protocol to be executed separately for all non_bb clashing ligand rotamers.
  Default: "default_lig"
  

  -start_from_random_rb_conf <Boolean>

  In the EnzdesFixBB protocol, if there are additional ligand rigid body conformations available (from a multimodel pdb), a random one of these will be the starting point for the protocol.
  Default: false
  

  -bb_bump_cutoff <Real>

  option to specify the maximum allowed backbone energie when replacing a new residue type
  Default: 2.0
  

  -sc_sc_bump_cutoff <Real>

  option to specify the maximum allowed energy between two newly placed sidechains in the secondary matcher
  Default: 2.0
  

  -no_packstat_calculation <Boolean>

  will determine whether the computationally intensive packstat calculation will be done at the end of a run
  Default: false
  

  -compare_native <String>

  triggers comparison of every designed structure to its respective native pdb. the value of the option needs to be a directory path that contains all the native pdb files
  Default: "./"
  

  -final_repack_without_ligand <Boolean>

  if a scorefile is requested, this option triggers every structure to be repacked without the ligand. the resulting structure will be output in a multimodel pdb, and differences in energy and rmsd are added to the scorefile.
  Default: false
  

  -dump_final_repack_without_ligand_pdb <Boolean>

  If option -final_repack_without_ligand is active, this option will cause the repacked structure to be separately dumped.
  Default: false
  

  -parser_read_cloud_pdb <Boolean>

  read cloud format PDB for enzdes in rosetta scripts
  Default: false
  

• packing

  -packing <Boolean>

  Packing option group
  

  -repack_only <Boolean>

  Disable design at all positions
  Default: false
  

  -prevent_repacking <Boolean>

  Disable repacking (or design) at all positions
  Default: false
  

  -ndruns <Integer>

  Number of fixbb packing iterations. Each time packing occurs, it will pack this many times and return only the best result. Implemented at level of PackRotamersMover.
  Range: 1-
  Default: 1
  

  -soft_rep_design <Boolean>

  Use larger LJ radii for softer potential
  

  -use_electrostatic_repulsion <Boolean>

  Use electrostatic repulsion
  

  -dump_rotamer_sets <Boolean>

  Output NMR-style PDB's with the rotamer sets used during packing
  

  -dunbrack_prob_buried <Real>

  fraction of possible dunbrack rotamers to include in each single residue rotamer set, for 'buried' residues
  Range: 0-1
  Default: 0.98
  

  -dunbrack_prob_nonburied <Real>

  fraction of possible dunbrack rotamers to include in each single residue rotamer set, for 'nonburied' residues
  Range: 0-1
  Default: 0.95
  

  -dunbrack_prob_nonburied_semirotameric <Real>

  fraction of possible dunbrack rotamers to include in each single residue rotamer set, for 'nonburied', semi-rotameric residues
  Range: 0-1
  Default: 0.95
  

  -no_optH <Boolean>

  Do not optimize hydrogen placement at the time of a PDB load
  Default: true
  

  -optH_MCA <Boolean>

  If running optH, use the Multi-Cool Annealer (more consistent, but slower)
  Default: false
  

  -pack_missing_sidechains <Boolean>

  Run packer to fix residues with missing sidechain density at PDB load
  Default: true
  

  -preserve_c_beta <Boolean>

  Preserve c-beta positions during rotamer construction
  

  -flip_HNQ <Boolean>

  Consider flipping HIS, ASN, and GLN during hydrogen placement optimization
  

  -fix_his_tautomer <IntegerVector>

  seqpos numbers of his residus whose tautomer should be fixed during repacking
  Default: []
  

  -print_pymol_selection <Boolean>

  include pymol-style selections when printing a PackerTask
  Default: false
  

• packing:ex1

  -ex1 <Boolean>

  use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

  -operate <Boolean>

  apply special operations (see RotamerOperation class) on ex1 rotamers
  

• packing:ex2

  -ex2 <Boolean>

  use extra chi2 sub-rotamers for all residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi2 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

  -operate <Boolean>

  apply special operations (see RotamerOperation class) on ex2 rotamers
  

• packing:ex3

  -ex3 <Boolean>

  use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi3 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

  -operate <Boolean>

  apply special operations (see RotamerOperation class) on ex3 rotamers
  

• packing:ex4

  -ex4 <Boolean>

  use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi4 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

  -operate <Boolean>

  apply special operations (see RotamerOperation class) on ex4 rotamers
  

• packing:ex1aro

  -ex1aro <Boolean>

  use extra chi1 sub-rotamers for aromatic residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

• packing:ex2aro

  -ex2aro <Boolean>

  use extra chi1 sub-rotamers for aromatic residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi2 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

• packing:ex1aro_exposed

  -ex1aro_exposed <Boolean>

  use extra chi1 sub-rotamers for all aromatic residues
  

  -level <Integer>

  use extra chi1 sub-rotamers for all aromatic residues The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

• packing:ex2aro_exposed

  -ex2aro_exposed <Boolean>

  use extra chi2 sub-rotamers for all aromatic residues
  

  -level <Integer>

  use extra chi2 sub-rotamers for all aromatic residues The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

• packing:exdna

  -exdna <Boolean>

  use extra dna rotamers
  

  -level <Integer>

  extra dna rotamer sample level -- rotbuilder converts from 0-7 to number
  Default: 1
  

• packing

  -extrachi_cutoff <Integer>

  number of neighbors a residue must have before extra rotamers are used. default: 18
  Default: 18
  

  -resfile <FileVector>

  resfile filename(s). Most protocols use only the first and will ignore the rest; it does not track against -s or -l automatically.
  Default: ['"resfile"']
  

  -outeriterations_scaling <Real>

  Multiplier for number of outer iterations
  Default: 1.0
  

  -inneriterations_scaling <Real>

  Multiplier for number of inner iterations
  Default: 1.0
  

  -explicit_h2o <Boolean>

  Use rotamers with explicit waters
  

  -adducts <StringVector>

  Gives list of adduct names to generate for residue definitions. Each adduct name may be followed by an optional integer, which gives a maximum number of adducts of that type which will be generated.
  

  -solvate <Boolean>

  Add explicit water, but don't try to place water such that it bridges Hbonds, just put it on every available Hbond donor/acceptor where there's no clash (implies explicit_h2o)
  

  -use_input_sc <Boolean>

  Use rotamers from input structure in packing By default, input sidechain coords are NOT included in rotamer set but are discarded before the initial pack; with this flag, the the input rotamers will NOT be discarded. Note that once the starting rotamers are replaced by any mechanism, they are no longer included in the rotamer set (rotamers included by coordinates)
  

  -unboundrot <FileVector>

  Read 'native' rotamers from supplied PDB(s). Unlike -use_input_sc, these rotamers will not be lost during repacks. This option requires specific support from the protocol; it is NOT built in to PackerTask.initialize_from_command_line()
  

  -max_rotbump_energy <Real>

  discard rotamers with poor interactions with the background using the specified cutoff. Values must be in the range of 0 to 5.0.
  Default: 5.0
  

  -lazy_ig <Boolean>

  Force the packer to always allocate pair energy storage but procrastinate energy caclulation until each RPE is needed; each RPE is computed at most once. Memory use is quadratic in rotamers per residue. The InteractionGraphFactory will prefer the linear-memory interaction graph to the Lazy Interaction graph, so specifying both linmem_ig and lazy_ig results in the use of the linear-memory interaction graph. The Surface-series IGs (surface weight in scorefunction is nonzero) also overrides this IG.
  Default: false
  

  -double_lazy_ig <Boolean>

  Force the packer to always procrastinate allocation AND energy caclulation until each RPE is needed; each RPE is computed at most once. The InteractionGraphFactory will prefer the linear-memory interaction graph to the DoubleLazy Interaction graph, so specifying both linmem_ig and lazy_ig results in the use of the linear-memory interaction graph. The Surface-series IGs (surface weight in scorefunction is nonzero) also overrides this IG.
  Default: false
  

  -double_lazy_ig_mem_limit <Integer>

  The amount of memory, in MB, that each double-lazy interaction graph should be allowed to allocate toward rotamer pair energies. Using this flag will not trigger the use of the double-lazy interaction graph, and this flag is not read in the PackerTask's initialize_from_command_line routine. For use in multistate design
  Default: 0
  

  -linmem_ig <Integer>

  Force the packer to use the linear memory interaction graph; each RPE may be computed more than once, but recently-computed RPEs are reused. The integer parameter specifies the number of recent rotamers to store RPEs for. 10 is the recommended size. Memory use scales linearly with the number of rotamers at about 200 bytes per rotamer per recent rotamers to store RPEs for (~4 KB per rotamer by default)
  Default: 10
  

  -multi_cool_annealer <Integer>

  Alternate annealer for packing. Runs multiple quence cycles in a first cooling stage, and tracks the N best network states it observes. It then runs low-temperature rotamer substitutions with repeated quenching starting from each of these N best network states. 10 is recommended.
  

  -minpack_temp_schedule <RealVector>

  Alternate annealing schedule for min_pack.
  

  -minpack_inner_iteration_scale <Integer>

  The number of inner iterations per rotamer to run at each temperature in min pack.
  

  -minpack_disable_bumpcheck <Boolean>

  Disable bump check in min pack (i.e. include rotamers that collide with the background.
  

• phil

  -phil <Boolean>

  phil option group
  

  -nloop <Integer>

  No description
  Default: 10
  

  -vall_file <String>

  No description
  

  -align_file <String>

  No description
  

• wum

  -wum <Boolean>

  wum option group
  

  -n_slaves_per_master <Integer>

  A value between 32 and 128 is usually recommended
  Default: 64
  

  -n_masters <Integer>

  Manual override for -n_slaves_per_master. How many master nodes should be spawned ? 1 by default. generall 1 for eery 256-512 cores is recommended depending on master workload
  Default: 1
  

  -memory_limit <Integer>

  Memory limit for queues (in kB)
  Default: 0
  

• lh

  -lh <Boolean>

  lh option group
  

  -db_prefix <String>

  stem for loop database
  Default: "loopdb"
  

  -loopsizes <IntegerVector>

  Which loopsizes to use
  Default: ['10', '15', '20']
  

  -num_partitions <Integer>

  Number of partitions to split the database into
  Default: 1
  

  -db_path <Path>

  Path to database
  Default: ""
  

  -exclude_homo <Boolean>

  Use a homolog exclusion filter
  Default: false
  

  -homo_file <String>

  File containing homologs to exclude
  Default: ""
  

  -skim_size <Integer>

  No description
  Default: 100
  

  -rounds <Integer>

  No description
  Default: 100
  

  -jobname <String>

  Prefix (Ident string) !
  Default: "default"
  

  -max_lib_size <Integer>

  No description
  Default: 2
  

  -max_emperor_lib_size <Integer>

  No description
  Default: 25
  

  -library_expiry_time <Integer>

  No description
  Default: 2400
  

  -mpi_resume <String>

  Prefix (Ident string) for resuming a previous job!
  

  -mpi_feedback <String>

  No description
  Default: "no"
  

  -mpi_batch_relax_chunks <Integer>

  No description
  Default: 100
  

  -mpi_batch_relax_absolute_max <Integer>

  No description
  Default: 300
  

  -mpi_outbound_wu_buffer_size <Integer>

  No description
  Default: 60
  

  -mpi_loophash_split_size <Integer>

  No description
  Default: 50
  

  -mpi_metropolis_temp <Real>

  No description
  Default: 1000000.0
  

  -mpi_save_state_interval <Integer>

  No description
  Default: 1200
  

  -max_loophash_per_structure <Integer>

  No description
  Default: 1
  

  -rms_limit <Real>

  How to deal with returned relaxed structures
  Default: 2.0
  

  -centroid_only <Boolean>

  false
  Default: false
  

  -write_centroid_structs <Boolean>

  Output raw loophashed decoys as well as relaxed ones
  Default: false
  

  -sandbox <Boolean>

  Sand box mode
  Default: false
  

  -create_db <Boolean>

  Make database with this loopsize
  Default: false
  

• blivens

  -blivens <Boolean>

  blivens option group
  

• blivens:disulfide_scorer

  -disulfide_scorer <Boolean>

  disulfide_scorer option group
  

  -nds_prob <Real>

  The probability of scoring a non-disulfide pair
  Default: 0.0
  

  -cys_prob <Real>

  The probability of outputing a pair of non-disulf cysteines. Default to nds_prob
  Default: -1.0
  

• blivens

  -score_type <String>

  The scoring type to use, eg for a filter.
  Default: "total_score"
  

• krassk

  -krassk <Boolean>

  krassk option group
  

  -left_tail <Integer>

  No description
  Default: 0
  

  -right_tail <Integer>

  No description
  Default: 0
  

  -tail_mode <Boolean>

  No description
  Default: false
  

  -tail_mode_name <Integer>

  No description
  Default: 1
  

  -tail_output_file_name <String>

  No description
  Default: "tail_output"
  

• robert

  -robert <Boolean>

  robert option group
  

  -pairdata_input_pdb_list <String>

  Takes in a file containing a list of pdb locations paired with protocol specific data (eg: one disulfide pair)
  Default: ""
  

  -pcs_maxsub_filter <Real>

  minimum normalized maxsub for PCS clustering protocol
  Default: 0.9
  

  -pcs_maxsub_rmsd <Real>

  maxsub calculation's rmsd threshold
  Default: 4.0
  

  -pcs_dump_cluster <Boolean>

  No description
  Default: false
  

• james

  -james <Boolean>

  james option group
  

  -dist_thresholds <RealVector>

  No description
  Default: utility::vector1<float>(1, 1.0)
  

  -torsion_thresholds <RealVector>

  No description
  Default: utility::vector1<float>(1, 30.0)
  

  -sog_cutoff <Real>

  No description
  Default: 5.0
  

  -shift_sog_func <Boolean>

  No description
  Default: true
  

  -min_type <String>

  No description
  Default: "dfpmin_armijo_nonmonotone"
  

  -min_tol <Real>

  No description
  Default: 0.0001
  

  -debug <Boolean>

  No description
  Default: false
  

  -real <Real>

  Option for keeping things real.
  Default: 7.0
  

  -n_designs <Integer>

  total number of designs that James should make.
  Default: 1
  

  -awesome_mode <Boolean>

  activates or deactivates awesome_mode.
  Default: true
  

  -n_clusters <Integer>

  number of clusters for k-means clustering.
  Default: 10
  

  -thread_unaligned <Boolean>

  basic_threading without performing an alignment
  Default: false
  

• membrane

  -membrane <Boolean>

  membrane option group
  

  -normal_cycles <Integer>

  number of membrane normal cycles
  Default: 100
  

  -normal_mag <Real>

  magnitude of membrane normal angle search (degrees)
  Default: 5
  

  -center_mag <Real>

  magnitude of membrane normal center search (Angstroms)
  Default: 1
  

  -smooth_move_frac <Real>

  No description
  Default: 0.5
  

  -no_interpolate_Mpair <Boolean>

  No description
  Default: false
  

  -Menv_penalties <Boolean>

  No description
  Default: false
  

  -Membed_init <Boolean>

  No description
  Default: false
  

  -Fa_Membed_update <Boolean>

  No description
  Default: false
  

  -center_search <Boolean>

  perform membrane center search
  Default: false
  

  -normal_search <Boolean>

  perform membrane normal search
  Default: false
  

  -center_max_delta <Integer>

  magnitude of maximum membrane width deviation during membrane center search (Angstroms)
  Default: 5
  

  -normal_start_angle <Integer>

  magnitude of starting angle during membrane normal search (degrees)
  Default: 10
  

  -normal_delta_angle <Integer>

  magnitude of angle deviation during membrane normal search (degrees)
  Default: 10
  

  -normal_max_angle <Integer>

  magnitude of maximum angle deviation during membrane normal search (degrees)
  Default: 40
  

  -debug <Boolean>

  No description
  Default: false
  

  -fixed_membrane <Boolean>

  fix membrane position, by default the center is at [0,0,0] and membrane normal is the z-axis
  Default: false
  

  -membrane_center <RealVector>

  membrane center x,y,z
  

  -membrane_normal <RealVector>

  membrane normal x,y,z
  

  -view <Boolean>

  viewing pose during protocol
  Default: false
  

• casp

  -casp <Boolean>

  casp option group
  

  -decoy <String>

  No description
  

  -wt <String>

  No description
  

  -rots <String>

  No description
  

  -opt_radius <Real>

  optimization radius for repacking and minimization
  

  -repack <Boolean>

  should we repack the structure?
  

  -sc_min <Boolean>

  should we sidechain minimize the structure?
  

  -sequential <Boolean>

  should mutations be considered in sequence or all together?
  

  -num_iterations <Real>

  number of iterations to perform
  

  -weight_file <String>

  what weight-file to use?
  

  -refine_res <String>

  specifies file that contains which residues to refine
  

• pose_metrics

  -pose_metrics <Boolean>

  pose_metrics option group
  

  -atomic_burial_cutoff <Real>

  maximum SASA that is allowed for an atom to count as buried for the BuriedUnsatisfiedPolarsCalculator
  Default: 0.3
  

  -sasa_calculator_probe_radius <Real>

  the probe radius used in the SASA calculator (and thus implicitly in the BuriedUnsatisfiedPolarsCalculator
  Default: 1.4
  

  -interface_cutoff <Real>

  distance in angstroms (def. 10.0) for calculating what residues are at an interface via InterfaceNeighborDefinitionCalculator
  Default: 10.0
  

  -min_sequence_separation <Integer>

  minimum number of sequence positions that two residues need to be apart to count as nonlocal in the NonlocalContactsCalculator
  Default: 6
  

  -contact_cutoffE <Real>

  maximum interaction energy allowed between two residues to count as a contact in the NonlocalContactsCalculator
  Default: -1.0
  

  -neighbor_by_distance_cutoff <Real>

  distance in angstroms (def. 10.0) for calculating neighbors of a residue via NeighborByDistanceCalculator
  Default: 10.0
  

  -inter_group_neighbors_cutoff <Real>

  distance in angstroms (def. 10.0) for calculating interfaces between domains with InterGroupNeighborsCalculator
  Default: 10.0
  

• ddg

  -ddg <Boolean>

  ddg option group
  

  -avg_rot_cst_enrg <Boolean>

  No description
  Default: false
  

  -use_bound_cst <Boolean>

  No description
  Default: false
  

  -cap_rot_cst_enrg <Real>

  No description
  Default: false
  

  -opt_input_structure <Boolean>

  No description
  Default: false
  

  -pack_until_converge <Boolean>

  No description
  Default: false
  

  -no_constraints <Boolean>

  No description
  Default: false
  

  -apply_rot_cst_to_mutation_region_only <Real>

  No description
  

  -rot_cst_enrg_cutoff <Real>

  No description
  

  -use_rotamer_constraints_to_native <Boolean>

  No description
  Default: false
  

  -single_res_scoring <Boolean>

  No description
  

  -downweight_by_sasa <Boolean>

  No description
  

  -global <Boolean>

  No description
  

  -exclude_solvent_exposed_res <Boolean>

  No description
  

  -radius <Real>

  No description
  

  -wt <String>

  No description
  

  -mut <String>

  No description
  

  -suppress_checkpointing <Boolean>

  boinc specific options to suppress checkpointing behavior
  Default: false
  

  -wt_only <Boolean>

  option added to minirosetta app in order to produce only refinement in wt structures
  

  -mut_only <Boolean>

  options added to minirosetta app in order to produce refinement in only mutant structure
  

  -output_silent <Boolean>

  No description
  

  -minimization_scorefunction <String>

  No description
  

  -minimization_patch <String>

  No description
  

  -min_cst <Boolean>

  Following sidechain optimization in the packer, should we then proceed to minimize the backbone at all. Constraints will be used to keep the structure from moving too far.
  Default: true
  

  -lowest_x_decoys <Real>

  No description
  

  -local_opt_only <Boolean>

  No description
  Default: false
  

  -print_per_res_diff <Boolean>

  No description
  Default: false
  

  -mean <Boolean>

  No description
  

  -min <Boolean>

  No description
  

  -rb_restrict_to_mutsite_nbrs <Boolean>

  No description
  Default: false
  

  -no_bb_movement <Boolean>

  No description
  Default: false
  

  -initial_repack <Boolean>

  No description
  Default: false
  

  -rb_file <String>

  No description
  

  -interface_ddg <Integer>

  Calculate ddGs across an interface? Uses jump # specified for determining interface.
  Default: 0
  

  -ens_variation <Real>

  No description
  Default: 0.5
  

  -sc_min_only <Boolean>

  No description
  Default: true
  

  -min_cst_weights <String>

  No description
  Default: "standard"
  

  -opt_radius <Real>

  No description
  Default: 8.0
  

  -output_dir <String>

  No description
  Default: "./"
  

  -last_accepted_pose_dir <String>

  No description
  Default: "./"
  

  -min_with_cst <Boolean>

  Used in ensemble generation
  Default: false
  

  -temperature <Real>

  because I really dont know what the monte carlo temperature should be set to
  Default: 10
  

  -ramp_repulsive <Boolean>

  set fa_rep to 0.1, 0.33 of original value when minimizing in the minimization phase following packing
  Default: false
  

  -mut_file <String>

  alternate specification for mutations. File format described in fix_bb_monomer_ddg.cc above the read_in_mutations function
  

  -out_pdb_prefix <String>

  specifies the prefix assigned to output so that no overwriting happens
  

  -constraint_weight <Real>

  because that other option isnt working
  Default: 1.0
  

  -harmonic_ca_tether <Real>

  default CA tether for harmonic constraints
  Default: 2.0
  

  -iterations <Integer>

  specifies the number of iterations of refinement
  Default: 20
  

  -out <String>

  create output file of predicted ddgs
  Default: "ddg_predictions.out"
  

  -debug_output <Boolean>

  specify whether or not to write a whole bunch of debug statements to standard out
  Default: false
  

  -dump_pdbs <Boolean>

  specify whether or not to dump repacked wild-type and mutant pdbs
  Default: true
  

  -weight_file <String>

  specifies the weight-files to be used in calculations
  Default: "ddg.wts"
  

• murphp

  -murphp <Boolean>

  murphp option group
  

  -inv_kin_lig_loop_design_filename <String>

  input filename to be used for inv_kin_lig_loop_design
  

• motifs

  -motifs <Boolean>

  motifs option group
  

  -close_enough <Real>

  4-atom rmsd cutoff beyond which you don't bother trying an inverse rotamer
  Default: 1.0
  

  -max_depth <Integer>

  Maximum recursion depth - i.e., maximum number of motifs to incorporate
  Default: 1
  

  -list_motifs <FileVector>

  File(s) containing list(s) of PDB files to process
  

  -motif_filename <String>

  File containing motifs
  

  -BPData <String>

  File containing BuildPosition specific motifs and/or rotamers
  

  -list_dnaconformers <FileVector>

  File(s) containing list(s) of PDB files to process
  

  -target_dna_defs <StringVector>

  
  Default: ""
  

  -motif_build_defs <StringVector>

  
  Default: ""
  

  -motif_build_position_chain <String>

  
  Default: ""
  

  -motif_build_positions <IntegerVector>

  
  

  -r1 <Real>

  RMSD cutoff between motif anchor position and motif target position for allowing a particular motif rotamer to continue on to expand with DNA conformers
  Range: 0-
  Default: 4.5
  

  -r2 <Real>

  RMSD cutoff between motif anchor position and motif target position for accepting the motif
  Range: 0-
  Default: 1.1
  

  -z1 <Real>

  DNA motif specific: cutoff between motif target DNA position and standardized base for allowing a particular motif to continue on to expand with DNA conformers
  Range: 0-
  Default: 0.75
  

  -z2 <Real>

  DNA motif specific: cutoff between motif target DNA position and DNA conformer placed according to motif for accepting the pair of residues
  Range: 0-
  Default: 0.95
  

  -dtest <Real>

  DNA motif specific: cutoff between motif target DNA position and DNA conformer placed according to motif for accepting the pair of residues
  Range: 0-
  Default: 5.5
  

  -rotlevel <Integer>

  level of rotamer sampling for motif search
  Range: 1-
  Default: 5
  

  -num_repacks <Integer>

  number of cycles of dropping special_rot weight and design
  Range: 0-
  Default: 5
  

  -minimize <Boolean>

  whether or not to minimize the motifs toward the xtal structure DNA
  Default: true
  

  -minimize_dna <Boolean>

  whether or not to minimize DNA after every round of design with special_rot weight dropping
  Default: true
  

  -run_motifs <Boolean>

  whether or not to use motifs in DnaPackerMotif
  Default: true
  

  -expand_motifs <Boolean>

  whether or not to use expand (use all types) motifs in DnaPackerMotif
  Default: true
  

  -dump_motifs <Boolean>

  whether or not to output pdbs with the best rotamer/conformer for each motifs
  Default: true
  

  -quick_and_dirty <Boolean>

  quick motif run to get a list of all possible motifs before doing a real run
  Default: true
  

  -special_rotweight <Real>

  starting weight for the weight on motif rotamers
  Default: -40.0
  

  -output_file <String>

  name of output file for all the best motifs and rotamers
  

  -data_file <String>

  name of output file for any data about how many rotamers and motifs pass what tests, etc
  

  -constraint_max <Real>

  highest value for constraint score (before and after minimization) that results in the rotamer being dropped
  Range: 0-
  Default: 20.0
  

  -flex_sugar <Boolean>

  whether or not to add the flexible sugar, not using PB way of adding options
  Default: true
  

  -clear_bprots <Boolean>

  whether or not to clear the rotamers that were read in from a previous run and restart with only the motifs that were read in and the specified rotlevel
  Default: true
  

  -rots2add <Integer>

  number of rotamers to add to design from the MotifSearch for each amino acid type
  Range: 1-
  Default: 100
  

• constraints

  -constraints <Boolean>

  constraints option group
  

  -CA_tether <Real>

  default CA tether for harmonic constraints
  Default: 2.0
  

  -exit_on_bad_read <Boolean>

  exit if error is encountered reading constraints
  Default: false
  

  -cst_file <StringVector>

  constraints filename(s) for centoroid. When multiple files are given a *random* one will be picked.
  

  -cst_weight <Real>

  No description
  Default: 1.0
  

  -max_cst_dist <Real>

  No description
  Default: 12.0
  

  -cst_fa_file <StringVector>

  constraints filename(s) for fullatom. When multiple files are given a *random* one will be picked.
  

  -cst_fa_weight <Real>

  No description
  Default: 1.0
  

  -normalize_mixture_func <Boolean>

  No description
  Default: false
  

  -penalize_mixture_func <Boolean>

  No description
  Default: true
  

  -forest_file <File>

  file with constraintforest
  Default: ""
  

  -compute_total_dist_cst <Boolean>

  only relevant for debug: atom_pair_constraints during abinito depends on seq_sep, this computes also the score without regarding seq_sep
  Default: false
  

  -cull_with_native <Integer>

  if option is set all constraints that violate the native structure with more than X are thrown out!
  Default: 1
  

  -dump_cst_set <File>

  dump the cstset_ to file
  Default: ""
  

  -evaluate_max_seq_sep <IntegerVector>

  evaluate constraints to this seq-sep [vector]
  Default: 0
  

  -named <Boolean>

  enable named constraints to avoid problems with changing residue-types e.g., cutpoint-variants
  Default: false
  

  -no_cst_in_relax <Boolean>

  remove constraints for relax
  Default: false
  

  -no_linearize_bounded <Boolean>

  dont switch to linearized in BOUNDED func
  Default: false
  

  -pocket_constraint_weight <Real>

  Weight of the Pocket Constraint
  Default: 0
  

  -pocket_zero_derivatives <Boolean>

  Return zero for PocketConstaint derivatives
  Default: false
  

  -viol <Boolean>

  show violations
  Default: false
  

  -viol_level <Integer>

  how much detail for violation output
  Default: 1
  

  -viol_type <String>

  work only on these types of constraints
  Default: ""
  

  -sog_cst_param <Real>

  weight parameter for SOGFunc constraints
  Default: 0.0
  

  -epr_distance <Boolean>

  use epr distance potential
  Default: false
  

  -combine <Integer>

  combine constraints randomly into OR connected groups (Ambiguous). N->1
  Default: 1
  

  -combine_exclude_region <File>

  core-defintion file do not combine constraints that are core-core
  

  -skip_redundant <Boolean>

  skip redundant constraints
  Default: false
  

  -skip_redundant_width <Integer>

  radius of influence for redundant constraints
  Default: 2
  

• dna

  -dna <Boolean>

  dna option group
  

• dna:specificity

  -specificity <Boolean>

  specificity option group
  

  -params <RealVector>

  vector of real-valued params
  

  -frag_files <FileVector>

  files to collect frags from
  

  -exclude_bb_sc_hbonds <Boolean>

  No description
  Default: false
  

  -only_repack <Boolean>

  No description
  Default: false
  

  -design_DNA <Boolean>

  No description
  Default: false
  

  -run_test <Boolean>

  No description
  Default: false
  

  -soft_rep <Boolean>

  No description
  Default: false
  

  -dump_pdbs <Boolean>

  No description
  Default: false
  

  -fast <Boolean>

  No description
  Default: false
  

  -randomize_motif <Boolean>

  No description
  Default: false
  

  -Whack_elec <Real>

  No description
  Default: 0
  

  -Wdna_bs <Real>

  No description
  Default: 0
  

  -Wdna_bp <Real>

  No description
  Default: 0
  

  -minimize_tolerance <Real>

  No description
  Default: 0.001
  

  -weights_tag <String>

  No description
  

  -weights_tag_list <String>

  No description
  

  -min_type <String>

  No description
  Default: "dfpmin"
  

  -tf <String>

  No description
  

  -mode <String>

  No description
  

  -score_function <String>

  No description
  

  -pre_minimize <Boolean>

  No description
  Default: false
  

  -post_minimize <Boolean>

  No description
  Default: false
  

  -pre_pack <Boolean>

  No description
  Default: false
  

  -nloop <Integer>

  No description
  Default: 20
  

  -n_inner <Integer>

  No description
  

  -n_outer <Integer>

  No description
  

  -nstep_water <Integer>

  No description
  Default: 0
  

  -moving_jump <Integer>

  No description
  Default: 0
  

  -motif_begin <Integer>

  No description
  Default: 0
  

  -motif_size <Integer>

  No description
  Default: 0
  

  -pdb_pos <StringVector>

  list of one or more positions in the input pdb, eg: -pdb_pos 125:A 127:A 4:C
  Default: ""
  

  -methylate <StringVector>

  list of one or more positions in the input pdb to be methylated, eg: -methylate 125:A 127:A 4:C
  Default: ""
  

• dna:design

  -design <Boolean>

  design option group
  

  -output_initial_pdb <Boolean>

  write pdb file for loaded and scored input structure
  Default: false
  

  -output_unbound_pdb <Boolean>

  write out an unbound pdb if doing binding score calculations
  Default: false
  

  -z_cutoff <Real>

  distance along DNA-axis from designing DNA bases to allow amino acids to design
  Range: 0-
  Default: 3.5
  

  -protein_scan <String>

  single-residue scanning of protein residue types for binding and specificity scores
  Default: "ACDEFGHIKLMNPQRSTVWY"
  

  -checkpoint <String>

  write/read checkpoint files for higher-level protocols that proceed linearly for long periods of time. Provide a checkpoint filename after this option.
  Default: ""
  

  -minimize <Boolean>

  Perform minimization in DNA design mode.
  Default: false
  

  -iterations <Integer>

  
  Range: 1-
  Default: 1
  

  -bb_moves <String>

  
  Default: "ccd"
  

  -dna_defs <StringVector>

  
  Default: ""
  

  -dna_defs_file <String>

  
  Default: ""
  

  -preminimize_interface <Boolean>

  
  Default: false
  

  -prepack_interface <Boolean>

  
  Default: false
  

  -flush <Boolean>

  enable some tracer flushes in order to see more frequent output
  Default: false
  

  -nopdb <Boolean>

  use this flag to disable pdb output
  Default: false
  

  -nopack <Boolean>

  don't actually repack structures
  Default: false
  

  -more_stats <Boolean>

  No description
  Default: false
  

  -pdb_each_iteration <Boolean>

  No description
  Default: false
  

  -designable_second_shell <Boolean>

  No description
  Default: false
  

  -base_contacts_only <Boolean>

  No description
  Default: false
  

  -probe_specificity <Integer>

  Rapidly estimate the explicit specificity of DNA designs during fixed-backbone repacking
  Default: 1
  

• dna:design:specificity

  -specificity <Boolean>

  specificity option group
  

  -output_structures <Boolean>

  output structures for each sequence combination
  Default: false
  

  -include_dna_potentials <Boolean>

  include DNA potentials in calculations of DNA sequence specificity
  Default: false
  

• dna:design

  -reversion_scan <Boolean>

  Try to revert spurious mutations after designing
  Default: false
  

• dna:design:reversion

  -reversion <Boolean>

  reversion option group
  

  -dscore_cutoff <Real>

  limit for acceptable loss in energy
  Default: 1.5
  

  -dspec_cutoff <Real>

  limit for acceptable loss in specificity
  Default: -0.05
  

• dna:design

  -binding <Boolean>

  compute a protein-DNA binding energy
  Default: false
  

  -Boltz_temp <Real>

  temperature for Boltzmann calculations
  Default: 0.6
  

  -repack_only <Boolean>

  Do not allow protein sequences to mutate arbitrarily
  Default: false
  

  -sparse_pdb_output <Boolean>

  Output only coordinates that change relative to the input structure
  Default: false
  

• flxbb

  -flxbb <Boolean>

  flxbb option group
  

  -view <Boolean>

  viewing pose during protocol
  

  -ncycle <Integer>

  number of cycles of design and relax
  

  -constraints_sheet <Real>

  weight constraints between Ca atoms in beta sheet
  

  -constraints_NtoC <Real>

  weight constraints between N- and C- terminal CA atoms
  

  -filter_trial <Integer>

  number of filtering trial
  

  -filter_type <String>

  filter type name, currently only packstat is available
  

  -exclude_Met <Boolean>

  do not use Met for design
  

  -exclude_Ala <Boolean>

  do not use Ala for design
  

  -blueprint <File>

  blueprint file
  

  -movemap_from_blueprint <Boolean>

  viewing pose during protocol
  

• flxbb:layer

  -layer <String>

  design core, boundary, and surface with different aa types
  Default: "normal"
  

  -pore_radius <Real>

  sphere radius for sasa calculation
  

  -burial <Real>

  surface area when residues regarded as core
  

  -surface <Real>

  surface area when residues regarded as surface
  

• fldsgn

  -fldsgn <Boolean>

  fldsgn option group
  

  -view <Boolean>

  viewing pose during protocol
  

  -blueprint <FileVector>

  blueprint filename(s).
  Default: ['"blueprint"']
  

  -dr_cycles <Integer>

  design-refine cycles
  Default: 3
  

  -centroid_sfx <String>

  filename of the centroid score function to use,
  

  -centroid_sfx_patch <String>

  filename of the centroid score function patch to use,
  

  -fullatom_sfx <String>

  filename of the full-atom score function to use
  

  -fullatom_sfx_patch <String>

  filename of the full-atom score function patch to use
  

  -run_flxbb <Integer>

  run flxbb at the given stage
  

• rna

  -rna <Boolean>

  rna option group
  

  -minimize_rounds <Integer>

  The number of rounds of minimization.
  Default: 2
  

• cm

  -cm <Boolean>

  cm option group
  

  -start_models_only <Boolean>

  Make starting models only!
  Default: false
  

  -aln_format <String>

  No description
  Default: "general"
  

  -recover_side_chains <Boolean>

  recover side-chains
  Default: false
  

  -loop_mover <String>

  No description
  Default: "quick_ccd"
  

  -loop_close_level <Integer>

  level of aggressiveness to use in closing loops. The integers that follow flags specify how aggressively loops are rebuilt. Each option implies all non-zero levels below it, so that loop_close_level 2 implies level 1 as well. Meaning of the options are: NO_REBUILD 0 don't rebuild loops at all REBUILD_UNALIGNED 1 rebuild loops around unaligned regions REBUILD_CHAINBREAK 2 rebuild loops around chainbreaks REBUILD_EXHAUSTIVE 3 rebuild loops around regions with a chainbreak until no chainbreaks remain
  Default: 0
  

  -min_loop_size <Integer>

  Minimum size of loops to remodel when building threading models.
  Default: 5
  

  -max_loop_rebuild <Integer>

  Maximum number of times to try to rebuild a loop before giving up.
  Default: 10
  

  -loop_rebuild_filter <Real>

  Maximum score a structure must have after loop rebuilding.
  Default: 0
  

  -aln_length_filter_quantile <Real>

  Only use alignment lengths longer than the Xth quantile. e.g. setting this to 0.75 will only use the 25% longest alignments
  Default: 0.0
  

  -aln_length_filter <Integer>

  Only use alignment longer or equal to this length
  Default: -1
  

  -template_ids <StringVector>

  List of template identifiers to use in comparative modeling
  

  -ligand_pdb <File>

  Add a ligand to the system
  

  -seq_score <String>

  sequence-based scoring scheme used for generating alignments
  Default: "Simple"
  

  -aligner <String>

  algorithm for making sequence alignments
  

  -min_gap_open <Real>

  gap opening penalty for sequence alignments (usually negative)
  Default: -2.0
  

  -max_gap_open <Real>

  gap opening penalty for sequence alignments (usually negative)
  Default: -2.0
  

  -min_gap_extend <Real>

  gap extension penalty for sequence alignments (usually negative)
  Default: -0.2
  

  -max_gap_extend <Real>

  gap extension penalty for sequence alignments (usually negative)
  Default: -0.2
  

  -nn <Integer>

  number of neighbors to include in constraint derivation
  Default: 500
  

  -fr_temperature <Real>

  temperature to use during fragment-based refinement of structures
  Default: 2.0
  

  -ev_map <FileVector>

  Input file that maps pdbChains to blast e-values
  

  -hh_map <FileVector>

  Input file that maps pdbChains to hhsearch probabilities
  

• ms

  -ms <Boolean>

  ms option group
  

  -share_data <Boolean>

  share rotamers and energies between states -- valid only if state variability is defined rotamerically
  Default: false
  

  -verbose <Boolean>

  
  Default: false
  

  -restrict_to_canonical <Boolean>

  design only canonical residue types
  Default: false
  

  -pop_from_ss <Integer>

  generate starting sequence population based on single-state design results
  Default: 0
  

  -pop_size <Integer>

  genetic algorithm population size
  Default: 100
  

  -generations <Integer>

  number of genetic algorithm generations
  Default: 20
  

  -num_packs <Integer>

  number of repack trials per sequence/state combination
  Default: 1
  

  -numresults <Integer>

  number of top-fitness results to save for explicit reference at the end of multistate design
  Default: 1
  

  -anchor_offset <Real>

  energy offset from the energy of single-state design toward the target state -- used to generate an affinity anchor for fitness calculations
  Default: 5.0
  

  -Boltz_temp <Real>

  thermodynamic temperature to use for specificity calculations
  Default: 0.6
  

  -mutate_rate <Real>

  rate of mutation per position
  Default: 0.5
  

  -fraction_by_recombination <Real>

  fraction of the population that should be generated by recombination during the evolution stage
  Default: 0.5
  

• ms:checkpoint

  -checkpoint <Boolean>

  checkpoint option group
  

  -prefix <String>

  prefix to add to the beginning of checkpoint file names
  Default: ""
  

  -interval <Integer>

  frequency with which the entity checkpoint is written
  Default: 0
  

  -gz <Boolean>

  compress checkpoing files with gzip
  Default: false
  

  -rename <Boolean>

  rename checkpoint files after genetic algorithm completes
  Default: false
  

• loops

  -loops <Boolean>

  loop modeling option group
  Default: true
  

  -cen_weights <String>

  ScoreFunction weights file for centroid phase of loop-modeling
  Default: "cen_std"
  

  -cen_patch <String>

  ScoreFunction patch for for centroid phase of loop-modeling
  Default: "score4L"
  

  -input_pdb <File>

  template pdb file
  Default: "input_pdb"
  

  -loop_file <StringVector>

  Loop definition file(s). When multiple files are given a *random* one will be picked each time when this parameter is requested.
  

  -extended_loop_file <File>

  loop definition file for loops to be extended (used in abrelax)
  Default: "loop_file"
  

  -mm_loop_file <File>

  loop definition file
  Default: "loop_file"
  

  -fix_natsc <Boolean>

  fix sidechains in template region in loop modeling
  Default: false
  

  -refine_only <Boolean>

  perform full atom refinement only on loops
  Default: false
  

  -fa_input <Boolean>

  input structures are in full atom format
  Default: false
  

  -fast <Boolean>

  reduce number of simulation cycles in loop modeling
  Default: false
  

  -vall_file <File>

  vall database file
  Default: "vall_file"
  

  -frag_sizes <IntegerVector>

  lengths of fragments to be used in loop modeling
  Default: ['9', '3', '1']
  

  -frag_files <FileVector>

  fragment libraries files
  Default: ['"frag9"', '"frag3"', '"frag1"']
  

  -output_pdb <File>

  output model pdb file
  Default: "output.pdb"
  

  -debug <Boolean>

  No description
  Default: false
  

  -build_initial <Boolean>

  Precede loop-modeling with an initial round of just removing the missing densities and building simple loops
  Default: false
  

  -extended <Boolean>

  Force extended on loops, independent of loop input file
  Default: false
  

  -remove_extended_loops <Boolean>

  Before building any loops, remove all loops marked as extended
  Default: false
  

  -idealize_after_loop_close <Boolean>

  Run structure through idealizer after loop_closing
  Default: false
  

  -idealize_before_loop_close <Boolean>

  Run structure through idealizer before loop_closing
  Default: false
  

  -select_best_loop_from <Integer>

  Keep building loops until N and choose best (by score)
  Default: 1
  

  -build_attempts <Integer>

  Build attempts per growth attempt
  Default: 3
  

  -grow_attempts <Integer>

  Total loop growth attempts
  Default: 7
  

  -random_grow_loops_by <Real>

  Randomly grow loops by up to this number of residues on either side.
  Default: 0.0
  

  -accept_aborted_loops <Boolean>

  accept aborted loops
  Default: false
  

  -strict_loops <Boolean>

  Do not allow growing of loops
  Default: false
  

  -superimpose_native <Boolean>

  Superimpose the native over the core before calculating looprms
  Default: false
  

  -build_specific_loops <IntegerVector>

  Numbers of the loops to be built
  

  -random_order <Boolean>

  build in random order
  Default: false
  

  -build_all_loops <Boolean>

  build all loops(no skip)
  Default: false
  

  -fa_closure_protocol <Boolean>

  Abrelax uses FASlidingWindowLoopClosure...
  Default: false
  

  -combine_rate <Real>

  Combine successive loops at this rate
  Default: 0.0
  

  -remodel <String>

  
  Default: "no"
  

  -intermedrelax <String>

  
  Default: "no"
  

  -refine <String>

  method for performing full-atom refinement on loops
  Default: "no"
  

  -relax <String>

  
  Default: "no"
  

  -n_rebuild_tries <Integer>

  number of times to retry loop-rebuilding
  Default: 1
  

  -final_clean_fastrelax <Boolean>

  Add a final fastrelax without constraints
  Default: false
  

  -relax_with_foldtree <Boolean>

  keep foldtree during relax
  Default: false
  

  -constrain_rigid_segments <Real>

  Use Coordinate constraints on the non-loop regions
  Default: 0.0
  

  -loopscores <String>

  Calculate loopscores individually
  

  -timer <Boolean>

  Output time spent in seconds for each loop modeling job
  Default: false
  

  -vicinity_sampling <Boolean>

  only sample within a certain region of the current torsion values
  Default: false
  

  -vicinity_degree <Real>

  number of degrees to sample within current torsion values for vicinity sampling
  Default: 1.0
  

  -neighbor_dist <Real>

  CB distance cutoff for repacking, rotamer trails, and side-chain minimization during loop modeling. NOTE: values over 10.0 are effectively reduced to 10.0
  Default: 10.0
  

  -kic_max_seglen <Integer>

  maximum size of residue segments used in kinematic closure calculations
  Default: 12
  

  -kic_recover_last <Boolean>

  If true, do not recover lowest scoring pose after each outer cycle and at end of protocol in kic remodel and refine
  Default: false
  

  -kic_min_after_repack <Boolean>

  Should the kinematic closure refine protocol minimize after repacking steps
  Default: false
  

  -optimize_only_kic_region_sidechains_after_move <Boolean>

  Should we perform rotamer trials and minimization after every KIC move but only within the loops:neighbor_dist of the residues in the moved KIC segment. Useful to speed up when using very large loop definitions (like when whole chains are used for ensemble generation).
  Default: false
  

  -max_kic_build_attempts <Integer>

  Number of attempts at initial kinematic closure loop building
  Default: 100
  

  -remodel_kic_attempts <Integer>

  Number of kic attempts per inner cycle during perturb_kic protocol
  Default: 300
  

  -max_kic_perturber_samples <Integer>

  Maximum number of kinematic perturber samples
  Default: 2000
  

  -nonpivot_torsion_sampling <Boolean>

  enables sampling of non-pivot residue torsions when the kinematic loop closure segment length is > 3
  Default: true
  

  -extend_length <Integer>

  Number of alanine residues to append after cutpoint in loopextend app
  Range: 0-
  Default: 0
  

  -outer_cycles <Integer>

  outer cycles in fullatom loop refinement
  Range: 1-
  Default: 3
  

  -max_inner_cycles <Integer>

  maxium number of inner cycles in fullatom loop refinement
  Range: 1-
  Default: 1
  

  -repack_period <Integer>

  repack period during fullatom loop refinement
  Range: 1-
  Default: 20
  

  -repack_never <Boolean>

  option to disable repacking during loop movement
  Default: false
  

  -remodel_init_temp <Real>

  Initial temperature for loop rebuiding. Currently only supported in kinematic (KIC) mode
  Default: 2.0
  

  -remodel_final_temp <Real>

  Final temperature for loop rebuilding. Currently only supported in kinematic (KIC) mode
  Default: 1.0
  

  -refine_init_temp <Real>

  Initial temperature for loop refinement. Currently only supported in kinematic (KIC) mode
  Default: 1.5
  

  -refine_final_temp <Real>

  Final temperature for loop refinement. Currently only supported in kinematic (KIC) mode
  Default: 0.5
  

  -gapspan <Integer>

  when automatically identifying loop regions, this is the maximum gap length for a single loop
  Range: 1-
  Default: 6
  

  -spread <Integer>

  when automatically identifying loop regions, this is the number of neighboring residues by which to extend out loop regions
  Range: 1-
  Default: 2
  

  -kinematic_wrapper_cycles <Integer>

  maximum number of KinematicMover apply() tries per KinematicWrapper apply()
  Default: 20
  

  -alternative_closure_protocol <Boolean>

  use WidthFirstSliding...
  Default: false
  

  -chainbreak_max_accept <Real>

  accept all loops that have a lower cumulative chainbreak score (linear,quadratic(if present), and overlap)
  Default: 2.0
  

  -debug_loop_closure <Boolean>

  dump structures before and after loop closing
  Default: false
  

  -non_ideal_loop_closing <Boolean>

  allow small non-idealities at the chainbreak residue after loop-closing -- requires binary silent out
  Default: false
  

  -scored_frag_cycles <Real>

  cycle-ratio for scored_frag_cycles ( loop_size<10 ) after jumping-abinitio
  Default: 0.1
  

  -short_frag_cycles <Real>

  cycle-ratio for short_frag_cycles ( loop_size<10 ) after jumping-abinitio
  Default: 0.2
  

  -rmsd_tol <Real>

  rmsd tolerance to deviate from original pose
  Default: 10000.0
  

  -chain_break_tol <Real>

  acceptable tolerance for chain break score
  Default: 0.2
  

  -random_loop <Boolean>

  randomize loop stub positions
  Default: false
  

  -stealfrags <FileVector>

  StealFragPDBS
  

  -stealfrags_times <Integer>

  StealFragPDBS how many times ?
  Default: 1
  

  -coord_cst <Real>

  restraintweight
  Default: 0.0
  

  -skip_1mers <Real>

  rate at which you should skip a 1 mer insertion
  Default: 0.0
  

  -skip_3mers <Real>

  rate at which you should skip a 3 mer insertion
  Default: 0.0
  

  -skip_9mers <Real>

  rate at which you should skip a 9 mer insertion
  Default: 0.0
  

  -loop_model <Boolean>

  loop modeling option
  Default: false
  

  -score_filter_cutoff <Real>

  value for score filter
  Default: 1.0
  

  -loop_farlx <Boolean>

  do fullatom loop refinement
  Default: false
  

  -ccd_closure <Boolean>

  apply ccd closure
  Default: false
  

  -skip_ccd_moves <Boolean>

  when running in ccd_moves mode, dont actually do ccd_moves.. just do fragment insertions
  Default: false
  

  -no_randomize_loop <Boolean>

  Leave loop as it is
  Default: false
  

  -loops_subset <Boolean>

  pick subset of desired loops
  Default: false
  

  -num_desired_loops <Integer>

  number of desired loops
  Default: 1
  

  -loop_combine_rate <Real>

  skip rate for not combining a chosen loop
  Default: 0.0
  

  -final_score_filter <Real>

  Only output structures that score bette rthan that
  Default: 1000000.0
  

  -no_combine_if_fail <Boolean>

  combine loops if loop modeling fails
  Default: true
  

  -shorten_long_terminal_loop <Boolean>

  shorten long loops
  Default: false
  

  -backrub_trials <Integer>

  number of backrub steps to do in loop relax
  Default: 10
  

  -looprlx_cycle_ratio <Real>

  fraction of the total looprlx cycles
  Default: 1.0
  

  -extended_beta <Real>

  Extended tempfactor: stochastic extendedness: p_ext = exp( - beta * length )
  Default: -1.0
  

  -shortrelax <Boolean>

  do a short fullatom relax after loop remodeling
  Default: false
  

  -fastrelax <Boolean>

  do a fast fullatom relax after loop remodeling
  Default: false
  

  -no_looprebuild <Boolean>

  do not rebuild loops
  Default: false
  

  -allow_lig_move <Boolean>

  allow ligands to move during loop modeling
  Default: false
  

  -keep_natro <File>

  list of residues where the rotamers are kept fixed
  Default: "keep_natro"
  

  -refine_design_iterations <Integer>

  iterations of refine and design
  Default: 1
  

• assembly

  -assembly <Boolean>

  assembly option group
  

  -pdb1 <File>

  pdb1 file
  

  -pdb2 <File>

  pdb2 file
  

  -nterm_seq <String>

  extra sequence at Nterminus
  Default: ""
  

  -cterm_seq <String>

  extra sequence at Cterminus
  Default: ""
  

  -linkers_pdb1 <IntegerVector>

  Residue numbers to be built as linkers
  

  -linkers_pdb2 <IntegerVector>

  Residue numbers to be built as linkers
  

  -preserve_sidechains_pdb1 <IntegerVector>

  Residue numbers to be sidchain-preserved
  

  -preserve_sidechains_pdb2 <IntegerVector>

  Residue numbers to be sidchain-preserved
  

• fast_loops

  -fast_loops <Boolean>

  fast_loops option group
  

  -window_accept_ratio <Real>

  windows with more than x percent of good loops in fast-loop sampling are used for scored-sampling
  Default: 0.0
  

  -nr_scored_sampling_passes <Integer>

  good windows go into scored-sampling N times
  Default: 4
  

  -nr_scored_fragments <Integer>

  scored loops sampled per good window each pass
  Default: 10
  

  -min_breakout_good_loops <Integer>

  stop doing scored sampling if N or more good loops have been found
  Default: 5
  

  -min_breakout_fast_loops <Integer>

  stop doing fast sampling if N or more good loops have been found
  Default: 40
  

  -min_good_loops <Integer>

  treat as failure if less good-loops than
  Default: 0
  

  -min_fast_loops <Integer>

  treat as failure if less fast-loops than
  Default: 3
  

  -vdw_delta <Real>

  accept as good loop if vdw-score < vdw-score-start+vdw-delta
  Default: 0
  

  -give_up <Integer>

  if N scored_frag_attemps didnt give any good loop -- jump out
  Default: 50
  

  -chainbreak_max <Real>

  accept only loops that have a maximum chainbreak score of... (sum of linear_chainbreak / chainbreak and overlap_chainbreak
  Default: 0.2
  

  -fragsample_score <File>

  Scorefunction used durgin scored-frag sampling
  Default: "loop_fragsample.wts"
  

  -fragsample_patch <File>

  Patch weights for scorefunction used during scored-frag sampling
  

  -overwrite_filter_scorefxn <File>

  force Scorefunction to be used during filter stage (instead last score of sampling protocol)
  

  -patch_filter_scorefxn <File>

  apply patch to Scorefunction used during filter stage
  

  -filter_cst_file <File>

  use these constraints to filter loops --- additional to whatever is in pose already
  

  -filter_cst_weight <Real>

  weight for constraints versus normal score (might contain additional constraints)
  Default: 1.0
  

  -fast_relax_sequence_file <File>

  use this FastRelax protocol for loop-selection
  

• SSrbrelax

  -SSrbrelax <Boolean>

  SSrbrelax option group
  

  -input_pdb <File>

  input pdb file
  Default: "input_pdb"
  

  -rb_file <File>

  rb definition file
  Default: "rb_file"
  

  -rb_param_file <File>

  rb param file
  Default: "rb_param_file"
  

  -frag_sizes <IntegerVector>

  lengths of fragments to be used in loop modeling
  Default: ['9', '3', '1']
  

  -frag_files <FileVector>

  fragment libraries files
  Default: ['"FragFile9"', '"FragFile3"', '"FragFile1"']
  

• boinc

  -boinc <Boolean>

  boinc option group
  

  -graphics <Boolean>

  The boinc client uses this option for the windowed graphics
  Default: false
  

  -fullscreen <Boolean>

  The boinc client uses this option for the screensaver full screen graphics
  Default: false
  

  -max_fps <Integer>

  Maximum frames per second, overrides user preference.
  Default: 0
  

  -max_cpu <Integer>

  Maximum cpu percentage, overrides user preferecne.
  Default: 0
  

  -noshmem <Boolean>

  for testing graphics without shared memory.
  Default: false
  

  -cpu_run_time <Integer>

  Target cpu run time in seconds
  Default: 10800
  

  -max_nstruct <Integer>

  Maximum number of output models (failed or successful) for a given client
  Default: 99
  

  -cpu_frac <Real>

  Percentage of CPU time used for graphics
  Default: 10.0
  

  -frame_rate <Real>

  Number of frames per second for graphics
  Default: 10.0
  

  -watchdog <Boolean>

  Turn watchdog on
  Default: false
  

  -watchdog_time <Integer>

  Time interval in seconds used by watchdog to check if run is stuck or going too long (default every 5 minutes)
  Default: 300
  

  -cpu_run_timeout <Integer>

  Maximum time the WU may exceed the users WU time settings. Default is 4 hours. Used by watchdog.
  Default: 14400
  

  -description_file <File>

  work unit description file
  Default: "rosetta_description.txt"
  

• LoopModel

  -LoopModel <Boolean>

  LoopModel option group
  

  -input_pdb <File>

  input pdb file
  Default: "LoopModel::input_pdb"
  

  -loop_file <File>

  input loops list file
  Default: "LoopModel::loop_file"
  

• AnchoredDesign

  -AnchoredDesign <Boolean>

  AnchoredDesign option group
  

  -anchor <File>

  anchor specification file
  Default: "anchor"
  

  -allow_anchor_repack <Boolean>

  allow repacking of anchor (default is to prevent)
  Default: false
  

  -vary_cutpoints <Boolean>

  vary loop cutpoints. Picks new cutpoints at start of each nstruct
  Default: false
  

  -no_frags <Boolean>

  use no fragments. Overrides passing an old-style fragment file. Skips new-style fragment generation.
  Default: false
  

  -debug <Boolean>

  debug mode (extra checks and pdb dumps)
  Default: false
  

  -show_extended <Boolean>

  dump pre-perturb PDB to check if loop torsions are extended
  Default: false
  

  -refine_only <Boolean>

  refine only mode (skip perturbation step)
  Default: false
  

  -perturb_show <Boolean>

  dump perturbed centroid pdbs as well as final results
  Default: false
  

  -perturb_cycles <Integer>

  perturbation phase runs for <input> cycles
  Default: 5
  

  -perturb_temp <Real>

  perturbation phase temperature for monte carlo
  Default: 0.8
  

  -perturb_CCD_off <Boolean>

  CCD-style loop remodeling off in perturb phase (meaning, KIC only)
  Default: false
  

  -perturb_KIC_off <Boolean>

  KIC-style loop remodeling off in perturb phase (meaning, CCD only)
  Default: false
  

  -refine_CCD_off <Boolean>

  CCD-style loop remodeling off in refine phase (meaning, KIC only)
  Default: false
  

  -refine_KIC_off <Boolean>

  KIC-style loop remodeling off in refine phase (meaning, CCD only)
  Default: false
  

  -refine_cycles <Integer>

  refinement phase runs for <input> cycles
  Default: 5
  

  -refine_temp <Real>

  refinement phase temperature for monte carlo
  Default: 0.8
  

  -refine_repack_cycles <Integer>

  refinement phase runs repack every <input> cycles
  Range: 2-
  Default: 20
  

  -rmsd <Boolean>

  Calculate result structure CA RMSD from starting structure
  Default: false
  

  -unbound_mode <Boolean>

  Ignore the anchor, as if this were loop modeling
  Default: false
  

  -chainbreak_weight <Real>

  Chainbreak term weight
  Default: 2.0
  

• AnchoredDesign:filters

  -filters <Boolean>

  filters option group
  

  -score <Real>

  do not print trajectories with scores greater than this total scorefunction value
  Default: 0
  

  -sasa <Real>

  do not print trajectories with sasas less than this interface delta sasa value
  Default: 500
  

  -omega <Boolean>

  filter out non-trans omegas
  Default: false
  

• AnchoredDesign:akash

  -akash <Boolean>

  akash option group
  

  -dyepos <Integer>

  dye position
  Default: 0
  

• AnchoredDesign:testing

  -testing <Boolean>

  testing option group
  

  -VDW_weight <Real>

  centroid VDW weight; testing if 2 better than 1
  Range: 0-
  Default: 1.0
  

  -anchor_via_constraints <Boolean>

  allow anchor&jump to move; anchor held in place via constraints - you must specify constraints!
  Default: false
  

• DenovoProteinDesign

  -DenovoProteinDesign <Boolean>

  DenovoProteinDesign option group
  

  -redesign_core <Boolean>

  redesign core of pdb
  Default: false
  

  -redesign_loops <Boolean>

  redesign loops of pdb
  Default: false
  

  -redesign_surface <Boolean>

  redesign surface of pdb
  Default: false
  

  -redesign_complete <Boolean>

  complete redesign of pdb
  Default: false
  

  -disallow_native_aa <Boolean>

  do not allow native aa in design
  Default: false
  

  -optimize_loops <Boolean>

  do serious loop modeling at the end of designrelax mover
  

  -secondary_structure_file <File>

  has fasta file format - describes secondary structure of desired target with H/C/E
  

  -hydrophobic_polar_pattern <File>

  has fasta file format - describes hydrophobic(B) polar(P) pattern
  

  -use_template_sequence <Boolean>

  use the template pdbs sequence when creating starting structures
  Default: false
  

  -use_template_topology <Boolean>

  use templates phi/psi in loops and begin/end helix/sheet generate only template like starting structures
  Default: false
  

  -create_from_template_pdb <File>

  create starting structure from a template pdb, follow with pdb name
  

  -create_from_secondary_structure <Boolean>

  create starting structure from a file that contains H/C/E to describe topology or B/P pattern, has fasta file format
  Default: false
  

• RBSegmentRelax

  -RBSegmentRelax <Boolean>

  RBSegmentRelax option group
  

  -input_pdb <File>

  input pdb file
  Default: "--"
  

  -rb_file <File>

  input rb segment file
  Default: "--"
  

  -cst_wt <Real>

  Weight on constraint term in scoring function
  Default: 0.1
  

  -cst_width <Real>

  Width of harmonic constraints on csts
  Default: 1.0
  

  -cst_pdb <String>

  PDB file from which to draw constraints
  Default: "--"
  

  -nrbmoves <Integer>

  number of rigid-body moves
  Default: 100
  

  -nrboutercycles <Integer>

  number of rigid-body moves
  Default: 5
  

  -rb_scorefxn <String>

  number of rigid-body moves
  Default: "score5"
  

  -skip_fragment_moves <Boolean>

  omit fragment insertions (in SS elements)
  Default: false
  

  -skip_seqshift_moves <Boolean>

  omit sequence shifting moves
  Default: false
  

  -skip_rb_moves <Boolean>

  omit rigid-body moves
  Default: false
  

  -helical_movement_params <RealVector>

  helical-axis-rotation, helical-axis-translation, off-axis-rotation, off-axis-translation
  Default: utility::vector1<float>(4,0.0)
  

  -strand_movement_params <RealVector>

  strand-in-plane-rotation, strand-in-plane-translation, out-of-plane-rotation, out-of-plane-translationn
  Default: utility::vector1<float>(4,0.0)
  

  -default_movement_params <RealVector>

  default-rotation, default-translation
  Default: utility::vector1<float>(2,0.0)
  

  -cst_seqwidth <Integer>

  sequence width on constraints
  Default: 0
  

• edensity

  -edensity <Boolean>

  edensity option group
  

  -debug <Boolean>

  No description
  Default: false
  

  -mapfile <String>

  No description
  

  -mapreso <Real>

  No description
  Default: 3.0
  

  -grid_spacing <Real>

  No description
  Default: 0.0
  

  -centroid_density_mass <Real>

  No description
  Default: 0.0
  

  -sliding_window <Integer>

  No description
  Default: 1
  

  -sliding_window_wt <Real>

  wt of edens sliding-window score
  Default: 0.0
  

  -whole_structure_ca_wt <Real>

  wt of edens centroid (CA-only) scoring
  Default: 0.0
  

  -whole_structure_allatom_wt <Real>

  wt of edens centroid (allatom) scoring
  Default: 0.0
  

  -no_edens_in_minimizer <Boolean>

  exclude density score from minimizer
  Default: false
  

  -debug_derivatives <Boolean>

  calculate numeric derivatives for density terms and compare with analytical
  Default: false
  

  -realign <String>

  how to initially align the pose to density
  Default: "no"
  

  -membrane_axis <String>

  the membrane normal axis
  Default: "Z"
  

  -atom_mask <Real>

  override default (=3.2A) atom mask radius to this value (hi-res scoring)
  Default: 3.2
  

  -ca_mask <Real>

  override default (=6A) CA mask radius to this value (low-res scoring)
  Default: 6.0
  

  -score_symm_complex <Boolean>

  If set, scores the structure over the entire symmetric complex; otherwise just use controlling monomer
  Default: false
  

  -sc_scaling <Real>

  Scale sidechain density by this amount (default 2/3 of mainchain density)
  Default: 0.6667
  

  -render_sigma <Real>

  initially render at this sigma level (extras=graphics build only)
  Default: 2
  

• patterson

  -patterson <Boolean>

  patterson option group
  

  -debug <Boolean>

  No description
  Default: false
  

  -weight <Real>

  wt of patterson correlation
  Default: 0.0
  

  -sc_scaling <Real>

  Scale sidechain density by this amount (default = same as mainchain density)
  Default: 1.0
  

  -radius_cutoffs <RealVector>

  patterson-space radius cuttoffs
  

  -resolution_cutoffs <RealVector>

  reciprocal space F^2 cuttoffs
  

  -Bsol <Real>

  solvent B
  Default: 300.0
  

  -Fsol <Real>

  solvent fraction
  Default: 0.95
  

  -model_B <Real>

  B factor computing patterson CC
  Default: 0.0
  

  -rmsd <Real>

  Expected RMS error for sigma-A calculation
  Default: 2.0
  

  -no_ecalc <Boolean>

  Do not normalize p_o with ecalc
  Default: false
  

  -nshells <Integer>

  Number of resolution shells for patterson normalization
  Default: 50
  

  -use_spline_interpolation <Boolean>

  use spline interpolation for derivative evaluation? (default trilinear)
  Default: false
  

  -use_on_repack <Boolean>

  SLOW - use patterson correlation on repacks (default no)
  Default: false
  

  -dont_use_symm_in_pcalc <Boolean>

  perform Pcalc in P1 (default no)
  Default: false
  

• optE

  -optE <Boolean>

  optE option group
  

  -data_in <String>

  file from which to read in optE data
  Default: "optE.data"
  

  -data_out <String>

  file to which to write optE data
  Default: "optE.data.out"
  

  -weights <String>

  a conventional weightfile that optE will use to determine which weights will be counted. All non-zero weights in the file will contribute to rotamer energies and be fit; use the -optE::fix option to fix any of these weights. Weight values will also be used as starting values for optimization.
  

  -fix <StringVector>

  weights to be fixed (must also appear in the weightfile given by the -optE::weights option)
  

  -free <File>

  IterativeOptEDriver flag: specify a file to read score types that are free -- optionally include a starting weight for each score type
  

  -fixed <File>

  IterativeOptEDriver flag: specify a file to read score types and weights for score types that are on but fixed
  

  -parse_tagfile <File>

  a file in utility::Tag format that optE may parse to customize its operation
  

  -constant_logic_taskops_file <File>

  a file in utility::Tag format that optE uses to build a task that will not change with the context of the pose after design
  

  -optE_soft_rep <Boolean>

  Instruct the IterativeOptEDriver to use the soft-repulsion etable
  

  -no_hb_env_dependence <Boolean>

  Disable environmental dependent weighting of hydrogen bond terms
  

  -no_hb_env_dependence_DNA <Boolean>

  Disable environmental dependent weighting of hydrogen bonds involving DNA
  

  -optE_no_protein_hack_elec <Boolean>

  Instruct the IterativeOptEDriver to use the soft-repulsion etable
  Default: false
  

  -design_first <Boolean>

  Do not optimize the weights in the context of the native structure, but rather, start by designing the protein with the input weight set. Requires that all score types listed in -optE::free have specificed weights.
  

  -n_design_cycles <Integer>

  The number of outer-loop design cycles to complete; default of 10 after which convergence has usually occurred
  Default: 10
  

  -recover_nat_rot <Boolean>

  With the iterative optE driver, repack to recover the native rotamers
  

  -component_weights <File>

  With the iterative optE driver, weight the individual components according to the input file -- default weight of 1 for all components. Weight file consists of component-name/weight pairs on separate lines: e.g. prob_native_structure 100.0
  

  -optimize_nat_aa <Boolean>

  With the iterative optE driver, optimize weights to maximize the probability of the native rotamer
  

  -optimize_nat_rot <Boolean>

  With the iterative optE driver, optimize weights to maximize the probability of the native rotamer in the native context
  

  -optimize_ligand_rot <File>

  With the iterative optE driver, optimize weights to maximize the probability of the native rotamer around the ligand
  

  -optimize_pssm <Boolean>

  With the iterative optE driver, optimize weights to maximize the match between a BLAST generated pssm probabillity distribution
  

  -optimize_dGbinding <File>

  With the iterative optE driver, optimize weights to minimize squared error between the predicted dG of binding and the experimental dG; provide a file listing 1. bound PDB structure, 2. unbound PDB structure, and 3. measured dG
  

  -optimize_ddG_bind_correlation <File>

  With the iterative optE driver, optimize weights to minimize squared error between the predicted ddG of binding for a mutation to the experimental ddG; provide a file listing 1. list file containing wt complexes, 2. list file containing mut complexes, 3. list file containing wt unbounds structures, 4. list file containing mut unbounds structures, and 5. measured ddG of binding
  

  -optimize_ddGmutation <File>

  With the iterative optE driver, optimize weights to minimize the predicted ddG of mutation and the measured ddG; provide a file listing 1. repacked wt pdb list, 2. repacked mut pdb list, and 3. measured ddG triples
  

  -optimize_ddGmutation_straight_mean <Boolean>

  With the iterative optE driver, predict the the ddGmut to be the difference between the straight mean (1/n Sum(E_i)) of the WT and MUT structures provided. Requires the -optimize_ddGmutation flag be set.
  

  -optimize_ddGmutation_boltzman_average <Boolean>

  With the iterative optE driver, predict the the ddGmut to be the difference between the boltzman average energies ( Sum( E_i * e**-E_i/kT)/Sum( e**-E_i/kT) ) of the WT and MUT structures provided. Requires the -optimize_ddGmutation flag be set.
  

  -exclude_badrep_ddGs <Real>

  With the iterative optE driver, consider only ddG data where the unweighted repulsive energy delta mut-wt < given value
  

  -pretend_no_ddG_repulsion <Boolean>

  With the iterative optE driver, set all repulsive scores to zero when looking for ddG correlations
  

  -optimize_decoy_discrimination <File>

  With the iterative optE driver, optimize weights to maximize the partition between relaxed natives and low-scoring decoys. File is a list of file-list pairs and a single pdb file < native_pdb_list, decoy_pdb_list, crystal_native_pdb >.
  

  -normalize_decoy_score_spread <String>

  In decoy discrimination optimization, normalize both the native and decoy energies generated by a set of weights by sigma_curr /sigma_start where sigma_start is computed as the standard deviation of the decoy energies given an input weight set
  

  -ramp_nativeness <Boolean>

  In decoy discrimination optimization, give structures in the range between max_rms_from_native and min_decoy_rms_to_native a nativeness score (which ramps linearly from 1 to 0 in that range) and include scores from structures in the numerator of the partition.
  

  -n_top_natives_to_optimize <Integer>

  For use with the -optimize_decoy_discrimination flag. Objective function considers top N natives in partition function
  Default: 1
  

  -approximate_decoy_entropy <Real>

  Alpha expansion of conformation space size as a function of nres: size ~ alpha ^ nres; entropy ~ nres ln alpha.
  

  -repack_and_minimize_decoys <Boolean>

  Generate new structures in each round of iterative optE by repacking and minimizing the input decoys & natives using the weights obtained in the last round
  

  -repack_and_minimize_input_structures <Boolean>

  Minimizing the input decoys & natives using the starting weights -- allows structures a chance to see the energy function before decoy discrimination begins without the memory overhead of the repack_and_minimize_decoys flag
  

  -output_top_n_new_decoys <Integer>

  For use with repack_and_minimize_decoys flag: Write out the top N decoys generated each round in this iterative refinement
  Default: 0
  

  -optimize_ligand_discrimination <File>

  With the iterative optE driver, optimize weights to maximize the partition between relaxed natives and low-scoring decoys. File is a list of file-list pairs and a single pdb file < native_pdb_list, decoy_pdb_list, crystal_native_pdb >.
  

  -no_design <Boolean>

  Don't bother loading pdbs and doing design; just optimize weights for decoy-discrim and or native rotamer recovery
  

  -sqrt_pssm <Boolean>

  Turn the pssm probability vectors into unit vectors so that dot product is a true similarity measure
  

  -min_decoy_rms_to_native <Real>

  For use with the optimize_decoy_discrimination flag: exclude decoys that are within a certain RMS of the native structure
  

  -max_rms_from_native <Real>

  For use with the optimize_decoy_discrimination flag: exclude natives that are more than a certain RMS of the crystal structure. max_rms_from_native of 1.5, min_decoy_rms_from_native 2.0 would throw out structures in the range of 1.5 and 2.0 RMS from consideration
  

  -optimize_starting_free_weights <Boolean>

  With the iterative optE driver, try many different starting points for the minimization
  Default: false
  

  -wrap_dof_optimization <File>

  Create new dofs and setup arithmetic dependencies for free dofs.
  

  -randomly_perturb_starting_free_weights <Real>

  With the iterative optE driver, perturb the weights by +/- <input value>=""> for those weights listed as free
  

  -inv_kT_natrot <Real>

  1 / kT for the pNativeRotamer fitness function
  Default: 1
  

  -inv_kT_nataa <Real>

  1 / kT for the pNatAA and PSSM fitness function
  Default: 1
  

  -inv_kT_natstruct <Real>

  1 / kT for the pNativeStructure fitness function
  Default: 1
  

  -mpi_weight_minimization <Boolean>

  Distribute OptEMultifunc func/dfunc evaluations across nodes
  

  -dont_use_reference_energies <Boolean>

  Do not use reference energies anywhere during the protocol.
  Default: false
  

  -number_of_swarm_particles <Integer>

  The number of particles to use during particle swarm weight optimization.
  Default: 100
  

  -number_of_swarm_cycles <Integer>

  The number of cycles to run the swarm minimizer for.
  Default: 20
  

  -constrain_weights <File>

  When minimizing the fitness objective function, also include weight constraints in the objective function
  

  -fit_reference_energies_to_aa_profile_recovery <Boolean>

  In the inner-loop sequence recovery/weight tweaking stage, accept/reject weight sets based on both the sequence recovery rate, and the mutual information between the expected and observed amino acid frequency distributions
  

  -repeat_swarm_optimization_until_fitness_improves <Boolean>

  After the first time though the particle swarm optimization phase, if the end fitness is not better than the start fitness, recreate the swarm around the start dofs and repeat the swarm optimization.
  Default: false
  

• optE:rescore

  -rescore <Boolean>

  rescore option group
  

  -weights <File>

  Weight set to use when rescoring optE partition functions
  

  -context_round <Integer>

  Integer of the context PDBs generated during design to use to measure the pNatAA
  

  -outlog <File>

  File to which the OptEPosition data should be written
  

  -measure_sequence_recovery <Boolean>

  When rescoring a weight set, run design with that weight set and measure the sequence recovery.
  Default: false
  

• backrub

  -backrub <Boolean>

  backrub option group
  

  -pivot_residues <IntegerVector>

  residues for which contiguous stretches can contain segments (internal residue numbers, defaults to all residues)
  Default: utility::vector1<int>()
  

  -pivot_atoms <StringVector>

  main chain atoms usable as pivots
  Default: utility::vector1<std::string>(1, "CA")
  

  -min_atoms <Integer>

  minimum backrub segment size (atoms)
  Default: 3
  

  -max_atoms <Integer>

  maximum backrub segment size (atoms)
  Default: 34
  

• bbg

  -bbg <Boolean>

  bbg option group
  

  -factorA <Real>

  Control how big the move would be(acceptance rate), default 1.0
  Default: 1.0
  

  -factorB <Real>

  Control how local the move would be(folded 10.0, unfolded 0.1), default 10.0
  Default: 10.0
  

  -ignore_improper_res <Boolean>

  Skip improper residues (proline)
  Default: false
  

  -fix_short_segment <Boolean>

  Do not apply small mover to short segments, for loop
  Default: false
  

• flexpack

  -flexpack <Boolean>

  flexpack option group
  

• flexpack:annealer

  -annealer <Boolean>

  annealer option group
  

  -inner_iteration_scale <Real>

  Scale up or down the number of inner iterations in the flexpack annealer
  

  -outer_iteration_scale <Real>

  Scale up or down the number of outer iterations in the flexpack annealer
  

  -fixbb_substitutions_scale <Real>

  Scale up or down the number of fixed-backbone rotamer substitutions in the flexpack annealer
  

  -pure_movebb_substitutions_scale <Real>

  Scale up or down the number of backbone moves
  

  -rotsub_movebb_substitutions_scale <Real>

  Scale up or down the number of rotamer substitions with backbone moves
  

• hotspot

  -hotspot <Boolean>

  hotspot option group
  

  -allow_gly <Boolean>

  Allow glycines in hotspot hashing constraints?
  Default: false
  

  -allow_proline <Boolean>

  Allow prolines in hotspot hashing constraints?
  Default: false
  

  -benchmark <Boolean>

  Score existing interface?
  Default: false
  

  -residue <StringVector>

  mini residue name3 to use for hotspot hashing
  Default: utility::vector1<std::string>(1,"ALL")
  

  -hashfile <File>

  Existing hotspot hash file.
  

  -target <File>

  Target PDB of the hotspot hash. Used for both de novo hashing and making hash density maps.
  

  -target_res <Integer>

  Rosetta residue number of interest on the target PDB. Used for targeted hashing
  

  -target_dist <Real>

  Tolerated distance from the target residue. Used for targeted hashing
  Default: 20
  

  -density <File>

  Filename to write *unweighted* hotspot density (compared to -target PDB).
  

  -weighted_density <File>

  Filename to write *score weighted* hotspot density (compared to -target PDB).
  

  -rms_target <File>

  Filename to write best rms of hotspot to target complex. Suitable for pymol data2b_res
  

  -rms_hotspot <File>

  Filename to write best rms of hotspot to target complex. Suitable for rms vs E scatter plots.
  

  -rms_hotspot_res <Integer>

  Rosetta residue # to use for calculating rms_hotspot.
  

  -rescore <Boolean>

  Rescore hotspots from -hashfile based on the supplied -target PDB.
  Default: false
  

  -threshold <Real>

  Score threshold for hotspot accepts. Found hotspots must be better than or equal to threshold
  Default: -1.0
  

  -sc_only <Boolean>

  Make backbone atoms virtual to find sidechain-only hotspots?
  Default: true
  

  -fxnal_group <Boolean>

  Only use a stubs functional group for rmsd calculations.
  Default: true
  

  -cluster <Boolean>

  Cluster stubset. Will take place before colonyE.
  Default: false
  

  -colonyE <Boolean>

  Rescore hotspots from -hashfile based on colony energy.
  Default: false
  

  -length <Integer>

  Length of hotspot peptide to use for hashing. Sidechain-containing group will be in the center.
  Default: 1
  

  -envhb <Boolean>

  Use environment dependent Hbonds when scoring hotspots.
  Default: false
  

  -angle <Real>

  Maximum allowed angle between stubCA, target CoM, and stubCB. Used to determine if stub is pointing towards target. Negative numbers deactivates this check (default)
  Default: -1
  

  -angle_res <Integer>

  Residue to use for angle calculation from stubCA, <this option>="">, and stubCB. Used to determine if stub is pointing towards target. 0 uses the default, which is the targets center of mass
  Default: 0
  

• parser

  -parser <Boolean>

  parser option group
  

  -protocol <String>

  File name for the xml parser protocol
  

  -script_vars <StringVector>

  Variable substitutions for xml parser, in the form of name=value
  

  -view <Boolean>

  Use the viewer?
  

  -patchdock <String>

  Patchdock output file name.
  

  -patchdock_random_entry <IntegerVector>

  Pick a random patchdock entry between two entry numbers. inclusive
  

• DomainAssembly

  -DomainAssembly <Boolean>

  DomainAssembly option group
  

  -da_setup <Boolean>

  run DomainAssembly setup routine
  Default: false
  

  -da_setup_option_file <File>

  input list of pdbs and linker sequences
  Default: "--"
  

  -da_setup_output_pdb <File>

  PDB file output by DomainAssemblySetup
  Default: "--"
  

  -da_linker_file <File>

  input file with linker definitions
  Default: "--"
  

  -da_start_pdb <File>

  input pdb for linker optimization
  Default: "--"
  

  -da_nruns <Integer>

  number of runs
  Default: 1
  

  -da_start_pdb_num <Integer>

  starting number for output pdb files
  Default: 1
  

  -da_linker_file_rna <File>

  input file with moveable RNA definitions
  Default: "--"
  

• remodel

  -remodel <Boolean>

  remodel option group
  

  -help <Boolean>

  help menu.
  

  -autopilot <Boolean>

  autopilot
  

  -blueprint <File>

  blueprint file name
  

  -cstfile <File>

  description
  

  -num_trajectory <Integer>

  Number of remodel trajectories.
  Default: 10
  

  -save_top <Integer>

  the number of final low scoring pdbs to keep.
  Default: 5
  

  -swap_refine_confirm_protocols <Boolean>

  swapping the protocols used refinement and confirmation
  Default: false
  

  -num_frag_moves <Integer>

  number of fragment moves to try in the centroid stage.
  

  -bypass_fragments <Boolean>

  only works on input PDB, so no extensions or deletions are honored in the blueprint. Blueprint (H,L,E,D) becomes allow_move definitionsi.
  

  -use_same_length_fragments <Boolean>

  harvest fragments that matches the length to rebuild
  Default: true
  

  -enable_ligand_aa <Boolean>

  handles ligand attachment and clash check after centroid build.
  

  -no_jumps <Boolean>

  will setup simple foldtree and fold through it during centroid build.
  

  -backrub <Boolean>

  run backrub MC trajectory after every completed loop building attempt
  

  -use_blueprint_sequence <Boolean>

  picks fragments based on both secondary structure and the second column (sequence) in blueprint file
  

  -randomize_equivalent_fragments <Boolean>

  will randomize identical scoring fragments; without either this flag or
  

  -quick_and_dirty <Boolean>

  only do fragment insertion
  

  -checkpoint <Boolean>

  this writes out the best pdbs collected so far after each design step.
  

  -use_ccd_refine <Boolean>

  maintain a default chainbreak position (loop start+1) and try using CCD for refinement. try 20 times for 5 closed loops.
  

  -use_pose_relax <Boolean>

  an alternative to the default minimization step, but use constraints in a similar way.
  

  -use_dssp_assignment <Boolean>

  use dssp assignment.
  

  -keep_jumps_in_minimizer <Boolean>

  no constraint is setup for minimization, only rebuilt regions allow bbmove.
  

  -output_fragfiles <File>

  output fragment file [filename ,e.g. aafr01].
  

  -read_fragfile <File>

  read fragment file.
  

  -generic_aa <String>

  the type of AA for centroid building
  Default: "VAL"
  

  -cluster_radius <Real>

  cluster radius for accumulator, default to auto set value
  Default: -1.0
  

  -use_clusters <Boolean>

  use clustering in accumulator
  Default: true
  

  -run_confirmation <Boolean>

  use KIC rms confirmation
  Default: false
  

  -cluster_on_entire_pose <Boolean>

  cluster use all pose, not just loops
  Default: false
  

  -collect_clustered_top <Integer>

  take the best N from each cluster
  Default: 1
  

  -dr_cycles <Integer>

  number of design-refine cycles to use
  Default: 3
  

  -two_chain_tree <Integer>

  label the start of the second chain
  

• remodel:domainFusion

  -domainFusion <Boolean>

  domainFusion option group
  

  -insert_segment_from_pdb <File>

  segment pdb file to be inserted [insert pdb file name].
  Default: ""
  

• remodel

  -hb_lrbb <Real>

  set hbond_lrbb weight
  Default: 0.0
  

  -hb_srbb <Real>

  set hbond_srbb weight
  Default: 0.0
  

  -rg <Real>

  set rg weight
  

  -rsigma <Real>

  set rsigma weight
  Default: 0.0
  

  -ss_pair <Real>

  set sspair weight
  Default: 0.0
  

  -build_disulf <Boolean>

  build disulfides
  Default: false
  

  -max_disulf_allowed <Integer>

  number of disulf pairs can be generated at a time
  Default: 1
  

  -match_rt_limit <Real>

  match RT score cutoff
  Default: 0.4
  

  -disulf_landing_range <IntegerVector>

  residue range for disulf landing sites
  

• remodel:design

  -design <Boolean>

  design option group
  

  -no_design <Boolean>

  skips all design steps. WARNING: will only output centroid level structures and dump all fragment tries.
  

  -silent <Boolean>

  dumps all structures by silent-mode WARNING: will work only during no_design protocol (see -no_design).
  

  -skip_partial <Boolean>

  skip design stage that operate only on burial positions
  Default: false
  

  -design_neighbors <Boolean>

  design neighbors.
  Default: false
  

  -find_neighbors <Boolean>

  find neighbors for design/repack
  Default: false
  

• remodel:RemodelLoopMover

  -RemodelLoopMover <Boolean>

  RemodelLoopMover option group
  

  -max_linear_chainbreak <Integer>

  linear chainbreak is <= this value, loop is considered closed (default 0.07)
  

  -randomize_loops <Boolean>

  randomize loops prior to running main protocol (default false)
  

  -allowed_closure_attempts <Integer>

  the allowed number of overall closure attempts (default 3)
  

  -simultaneous_cycles <Integer>

  the number of simultaneous closure cycles to perform (default 2)
  

  -independent_cycles <Integer>

  the number of independent closure cycles to perform (default 8)
  

  -lockdown_cycles <Integer>

  the maximum number of possible lockdown closure cycles to perform (default 30)
  

• remodel

  -rank_by_bsasa <Boolean>

  rank results by bsasa.
  

• fold_from_loops

  -fold_from_loops <Boolean>

  fold_from_loops option group
  

  -native_ca_cst <Boolean>

  derive constraints from the native topology
  Default: false
  

  -swap_loops <File>

  pdb of the target loops
  Default: "--"
  

  -checkpoint <String>

  write/read checkpoint files for nstruct. Provide a checkpoint filename after this option.
  Default: ""
  

  -ca_csts_dev <Real>

  standard deviation allowed to each constraint
  Default: 0.5
  

  -add_relax_cycles <Integer>

  additional relax cycles
  Default: 2
  

  -loop_mov_nterm <Integer>

  Movable region inside the provided loop(nterm)
  Default: 0
  

  -loop_mov_cterm <Integer>

  Moveable region inside the provided loop(cterm)
  Default: 0
  

  -ca_rmsd_cutoff <Real>

  Filter the decoys to pass the relax-design stage
  Default: 5.0
  

  -res_design_bs <IntegerVector>

  enumerate the residues to be designed within the fixed binding site
  

• symmetry

  -symmetry <Boolean>

  symmetry option group
  

  -symmetry_definition <String>

  Text file describing symmetry setup
  

  -initialize_rigid_body_dofs <Boolean>

  Initialize the RB dofs from the symmetry definition file?
  Default: false
  

  -perturb_rigid_body_dofs <RealVector>

  (As in docking) Do a small perturbation of the symmetric DOFs: -perturb_rigid_body_dofs ANGSTROMS DEGREES
  

  -symmetric_rmsd <Boolean>

  calculate the rmsd symmetrically by checking all chain orderings
  

• fold_and_dock

  -fold_and_dock <Boolean>

  fold_and_dock option group
  

  -move_anchor_points <Boolean>

  move the anchor points that define symmetric coordinate system during symmetry fragment insertion
  Default: false
  

  -set_anchor_at_closest_point <Boolean>

  set the anchor points that define symmetric coordinate system to the nearest point between two consecutive chains during fragment insertion
  Default: false
  

  -rotate_anchor_to_x <Boolean>

  rotate the anchor residue to the x-axis before applying rigid body transformations
  Default: false
  

  -trans_mag_smooth <Real>

  translation perturbation size for smooth refinement
  Default: 0.1
  

  -rot_mag_smooth <Real>

  rotational perturbation size for smooth refinement
  Default: 1.0
  

  -rb_rot_magnitude <Real>

  rotational perturbation size for rigid body pertubations
  Default: 8.0
  

  -rb_trans_magnitude <Real>

  translational perturbation size rigid body pertubations
  Default: 3.0
  

  -rigid_body_cycles <Integer>

  number of rigid bosy cycles during fold and dock fragment insertion
  Default: 50
  

  -rigid_body_frequency <Real>

  The fraction of times rigid body cycles are applied during fragment assembly moves
  Default: 0.2
  

  -rigid_body_disable_mc <Boolean>

  Dissallow moves to be accepted locally by MC criteria within the rigid body mover
  Default: false
  

  -slide_contact_frequency <Real>

  The fraction of times subunits are slided together during fragment assembly moves
  Default: 0.1
  

• match

  -match <Boolean>

  match option group
  

  -lig_name <String>

  Name of the ligand to be matched. This should be the same as the NAME field of the ligand's parameter file (the .params file)
  

  -bump_tolerance <Real>

  The permitted level of spherical overlap betweeen any two atoms. Used to detect collisions between the upstream atoms and the background, the upstream atoms and the downstream atoms, and the downstream atoms and the background
  Default: 0.0
  

  -active_site_definition_by_residue <File>

  File describing the active site of the scaffold as a set of resid/radius pairs
  

  -active_site_definition_by_gridlig <File>

  File containing 1s and Os describing the volume of space for the active site. .gridlig file format from Rosetta++
  

  -required_active_site_atom_names <File>

  File listing the downstream-residue-atom names which must reside in the defined active site. Requires either the flag active_site_definition_by_residue or the flag active_site_definition_by_gridlig to be specified.
  

  -grid_boundary <File>

  File describing the volume in space in which the third orientation atom must lie
  Default: ""
  

  -geometric_constraint_file <File>

  File describing the geometry of the downstream object relative to the upstream object
  

  -scaffold_active_site_residues <File>

  File with the residue indices on the scaffold that should be considered as potential launch points for the scaffold's active site. File format described in MatcherTask.cc in the details section of the initialize_scaffold_active_site_residue_list_from_command_line() method.
  Default: ""
  

  -scaffold_active_site_residues_for_geomcsts <File>

  File which lists the residue indices on the scaffold to consider as potential launch points for the scaffold's active site for each geometric constraint; each constraint may have a separate set of residue ids. File format described in MatcherTask.cc in the details section of the initialize_scaffold_active_site_residue_list_from_command_line() method.
  Default: ""
  

  -euclid_bin_size <Real>

  The bin width for the 3-dimensional coordinate hasher, in Angstroms
  Default: 1.0
  

  -euler_bin_size <Real>

  The bin width for the euler angle hasher, in degrees
  Default: 10.0
  

  -consolidate_matches <Boolean>

  Instead of outputting all matches, group matches and then write only the top -match::output_matches_per_group from each group.
  Default: false
  

  -output_matches_per_group <Integer>

  The number of matches to output per group. Requires the -match::consolidate_matches flag is active.
  Default: 10
  

  -orientation_atoms <StringVector>

  The three atoms, by name, on the downstream partner to use to describe its 6 dimensional coordinate; its position and orientation. Only usable when the downstream partner is a single residue. Exactly 3 atom names must be given. If these atoms are unspecified, the matcher will use the residues neighbor atom and two atoms bonded to the neighbor atom to define the orientation. The euclidean coordinate of the third orientation atom is used as the first the dimensions of the downstream residues 6D coordinate; the other three dimensions are the three euler angles described by creating a coordinate frame at orientation atom 3, with the z axis along the vector from orientation atom 2 to orientation atom 3, and the y axis lying in the plane with orientation atoms 1,2&3.
  

  -output_format <String>

  The format in which the matches are output
  Default: "CloudPDB"
  

  -match_grouper <String>

  The parameters that matches are grouped according to by the MatchConsolidator or the CloudPDBWriter
  Default: "SameSequenceAndDSPositionGrouper"
  

  -grouper_downstream_rmsd <Real>

  Maximum allowed rmsd between two orientations of the downstream pose to be considered part of the same group
  Default: 1.5
  

  -output_matchres_only <Boolean>

  Whether to output the matched residues only or the whole pose for every match
  Default: false
  

  -geom_csts_downstream_output <IntegerVector>

  For which of the geometric constraints the downstream residue/ligand will be output
  Default: ['1']
  

  -filter_colliding_upstream_residues <Boolean>

  Filter the output matches if the hits induce a collision between the upstream residues
  Default: true
  

  -upstream_residue_collision_tolerance <Real>

  The amount of atom overlap allowed between upstream residues in a match. If this is unspecified on the command line, then the value in the bump_tolerance option is used
  Default: 0.0
  

  -upstream_residue_collision_score_cutoff <Real>

  The score cutoff for upstream residue pairs to use in the collision filter. Activating this cutoff uses the etable atr/rep/sol terms to evaluate residue-pair interactions instead of hard-sphere overlap detection
  Default: 10.0
  

  -upstream_residue_collision_Wfa_atr <Real>

  The fa_atr weight to use in the upstream-collision filter; use in tandem with upstream_residue_collision_score_cutoff
  Default: 0.8
  

  -upstream_residue_collision_Wfa_rep <Real>

  The fa_rep weight to use in the upstream-collision filter; use in tandem with upstream_residue_collision_score_cutoff
  Default: 0.44
  

  -upstream_residue_collision_Wfa_sol <Real>

  The fa_sol weight to use in the upstream-collision filter; use in tandem with upstream_residue_collision_score_cutoff
  Default: 0.0
  

  -filter_upstream_downstream_collisions <Boolean>

  Filter the output matches if the hits induce a collision between the upstream residues and the downstream pose
  Default: true
  

  -updown_collision_tolerance <Real>

  The amount of atom overlap allowed between upstream and downstream atoms in a match. If this is unspecified on the command line, then the value in the bump_tolerance option is used
  Default: 0.0
  

  -updown_residue_collision_score_cutoff <Real>

  The score cutoff for upstream/downstream residue pairs to use in the collision filter. Activating this cutoff uses the etable atr/rep/sol terms to evaluate residue-pair interactions instead of hard-sphere overlap detection
  Default: 10.0
  

  -updown_residue_collision_Wfa_atr <Real>

  The fa_atr weight to use in the upstream-downstream-collision filter; use in tandem with updown_residue_collision_score_cutoff
  Default: 0.8
  

  -updown_residue_collision_Wfa_rep <Real>

  The fa_rep weight to use in the upstream-downstream-collision filter; use in tandem with updown_residue_collision_score_cutoff
  Default: 0.44
  

  -updown_residue_collision_Wfa_sol <Real>

  The fa_sol weight to use in the upstream-downstream-collision filter; use in tandem with updown_residue_collision_score_cutoff
  Default: 0.0
  

  -define_match_by_single_downstream_positioning <Boolean>

  Enumerate combinations of matches where a single positioning of the downstream partner as well as the conformations of the upstream residues defines the match; it is significantly faster to enumerate unique matches when they are defined this way instead of enumerating the (combinatorially many) matches when a match is defined by n-geometric-constraint locations of the downstream partner. This faster technique for outputting matches is automatically chosen when the flag -match::output_format is PDB.
  

  -ligand_rotamer_index <Integer>

  Match with a particular conformation of the ligand; the index represents which conformation in the multi-model .pdb file specified in the ligand's .params file by the PDB_ROTAMERS field. The index of the first conformation in that file is 1; valid indices range from 1 to the number of entries in the multi-model .pdb file. If this command-line flag is not used, then the conformation of the ligand described by the ICOOR_INTERNAL lines of the ligand's .params file is used instead.
  

  -enumerate_ligand_rotamers <Boolean>

  Match with all ligand rotamers specified in the multi-model .pdb file specified in the ligand's .params file by the PDB_ROTAMERS field. This flag may not be used in combination with the match::ligand_rotamer_index flag. Geometry of the ligand rotamers in the .pdb file will be idealized to the .params file bond angles and lengths.
  Default: true
  

  -only_enumerate_non_match_redundant_ligand_rotamers <Boolean>

  Only defined if enumerate_ligand_rotamers is true this option causes the matcher to determine which rotamers in the ligand rotamer library are redundant in terms of matching, meaning the atoms they're matched through are superimposable. after having subdivided the ligand rotamer library into match-redundant subgroups, the matcher will then only place the first nonclashing rotamer from each subgroup.
  Default: true
  

• rdc

  -rdc <Boolean>

  rdc option group
  

  -correct_NH_length <Boolean>

  fix N-H bond-vector to 1.04 as measured in ottiger&bax 98
  

  -reduced_couplings <Boolean>

  gives more equal weights to different bond-vectors
  

  -weights <File>

  specify weights for individual residues ( works for all couplings at this reside)
  

  -iterate_weights <Real>

  do a wRDC computation, i.e., iterate tensor calculation until weights are ~exp ( -dev2/sigma )
  Default: 1
  

  -segment_file <File>

  Definition of rigid segments for alignment tensor optimization
  

  -segment_scoring_mode <String>

  Type of treatment of alignment tensor-based scoring : pairwise or fixed_axis_z (e.g. for homo-dimers)
  

  -total_weight <Real>

  Weight for RDC scores of individual al. tensors
  Default: 1.0
  

  -tensor_weight <Real>

  Weight for pairwise scoring of al. tensors
  Default: 1.0
  

  -print_rdc_values <File>

  print computed vs experimental RDC values
  

  -iterate_tol <Real>

  tolerance for tensor iterations
  Default: 0.01
  

  -iterate_reset <Boolean>

  reset weights to 1.0 when optimizing for new structure
  Default: false
  

  -dump_weight_trajectory <File>

  if yes, write weights to file for each scoring event
  

  -fix_normAzz <RealVector>

  divide by this axial tensor component
  

  -select_residues_file <File>

  loop/rigid-file with RIGID entries that define the set of residues active for RDC score
  

• antibody

  -antibody <Boolean>

  Antibody option group
  

  -graft_l1 <Boolean>

  Graft CDR L1 from template
  Default: false
  

  -l1_template <String>

  Choose specified template for CDR L1 grafting
  Default: "l1.pdb"
  

  -graft_l2 <Boolean>

  Graft CDR L2 from template
  Default: false
  

  -l2_template <String>

  Choose specified template for CDR L2 grafting
  Default: "l2.pdb"
  

  -graft_l3 <Boolean>

  Graft CDR L3 from template
  Default: false
  

  -l3_template <String>

  Choose specified template for CDR L3 grafting
  Default: "l3.pdb"
  

  -graft_h1 <Boolean>

  Graft CDR H1 from template
  Default: false
  

  -h1_template <String>

  Choose specified template for CDR H1 grafting
  Default: "h1.pdb"
  

  -graft_h2 <Boolean>

  Graft CDR H2 from template
  Default: false
  

  -h2_template <String>

  Choose specified template for CDR H2 grafting
  Default: "h2.pdb"
  

  -graft_h3 <Boolean>

  Graft CDR H3 from template
  Default: false
  

  -h3_template <String>

  Choose specified template for CDR H3 grafting
  Default: "h3.pdb"
  

  -model_h3 <Boolean>

  Model CDR H3 from scratch using fragments
  Default: false
  

  -snugfit <Boolean>

  Adjust relative orientation of VL-VH
  Default: false
  

  -snug_loops <Boolean>

  Allow CDR loop backbone flexibility during minimization
  Default: false
  

  -input_fv <File>

  input antibody variable (Fv) region
  Default: "FR02.pdb"
  

  -camelid <Boolean>

  Camelid input with only heavy (VH) chain
  Default: false
  

  -camelid_constraints <Boolean>

  Display constraints file for use with camelid H3 modeler
  Default: false
  

• flexPepDocking

  -flexPepDocking <Boolean>

  flexPepDocking option group
  

  -params_file <String>

  parameters file that describe the complex details, like anchor residues, etc.
  

  -peptide_anchor <Integer>

  Set the peptide anchor residue mannualy (instead of using the center of mass
  Range: 1-
  Default: 1
  

  -receptor_chain <String>

  chain-id of receptor protein
  

  -peptide_chain <String>

  chain-id of peptide protein
  

  -lowres_abinitio <Boolean>

  Do a preemptive ab-initio low-resolution peptide docking
  Default: false
  

  -lowres_preoptimize <Boolean>

  Do a preemptive optimization in low resolution
  Default: false
  

  -flexPepDockingMinimizeOnly <Boolean>

  Just do simple minimization on input structure
  Default: false
  

  -extend_peptide <Boolean>

  start the protocol with the peptide in extended conformation
  Default: false
  

  -rbMCM <Boolean>

  Do rigid body mcm in the main loop of the protocol
  Default: false
  

  -torsionsMCM <Boolean>

  Do torsions (small/shear mcm in the main loop of the protocol
  Default: false
  

  -peptide_loop_model <Boolean>

  Do cycles of random loop modeling to peptide backbone
  Default: false
  

  -backrub_peptide <Boolean>

  Adds a backrub stage to the protocol
  Default: false
  

  -boost_fa_atr <Boolean>

  while ramping up the fa_rep, start from high atr and lower to normal
  Default: true
  

  -ramp_fa_rep <Boolean>

  Whether to ramp the full-atom repulsive score during the protocol
  Default: true
  

  -ramp_rama <Boolean>

  Whether to ramp the Ramachandran score during the protocol
  Default: false
  

  -flexpep_score_only <Boolean>

  just reads in the pose and scores it
  Default: false
  

  -ref_startstruct <File>

  Alternative start structure for scoring statistics, instead of the original start structure (useful as reference for rescoring previous runs)
  

  -use_cen_score <Boolean>

  when in score_only mode, uses centroid weights to score
  Default: false
  

  -design_peptide <Boolean>

  Add a desing stage to each cycle of the RB-torsions perturbations
  Default: false
  

  -rep_ramp_cycles <Integer>

  Number of cycles for the ramping up of repulsion term
  Range: 0-
  Default: 10
  

  -mcm_cycles <Integer>

  Number of cycles for the mcm procedures (rb/torsions)
  Range: 0-
  Default: 8
  

  -random_phi_psi_preturbation <Real>

  Size of random perturbation of peptide's phi/psi
  Range: 0.0-
  Default: 0.0
  

  -smove_angle_range <Real>

  Defines the perturbations size of small/sheer moves
  Range: 0.0-
  Default: 6.0
  

  -min_receptor_bb <Boolean>

  Whether to include protein backbone in minimization
  Default: false
  

  -random_trans_start <Real>

  Size of random perturbation of peptide's rigid body translation
  Range: 0.0-
  Default: 0.0
  

  -random_rot_start <Real>

  Size of random perturbation of peptide's rigid body rotation
  Range: 0.0-
  Default: 0.0
  

  -flexpep_prepack <Boolean>

  Prepack an initial structure and exit
  Default: false
  

  -flexpep_noprepack1 <Boolean>

  Do not repack the side-chains of partner 1 ( = globular protein).
  Default: false
  

  -flexpep_noprepack2 <Boolean>

  Do not repack the side-chains of partner 2 ( = peptide).
  Default: false
  

  -score_filter <Real>

  Only output decoys with scores lower than this filter.
  Default: 10000.0
  

  -hb_filter <Integer>

  Only output decoys with more h-bonds than this filter.
  Range: 0-
  Default: 0
  

  -hotspot_filter <Integer>

  Only output decoys with more hotspots than this filter.
  Range: 0-
  Default: 0
  

  -frag5 <String>

  5-mer fragments for ab-initio flexPepDock
  

• threadsc

  -threadsc <Boolean>

  threadsc option group
  

  -src_chain <String>

  Chain of source pdb
  

  -trg_chain <String>

  Chain of target pdb
  

  -src_first_resid <Integer>

  Residue id of first residue in source pdb range
  

  -trg_first_resid <Integer>

  Residue id of first residue in source pdb range
  

  -nres <Integer>

  Number of residues to be threaded
  

  -trg_anchor <Integer>

  anchor residue for backbone threading
  

• archive

  -archive <Boolean>

  archive option group
  

  -reread_all_structures <Boolean>

  ignore pool file... reread from batches
  Default: false
  

  -completion_notify_frequency <Integer>

  tell Archive every X completed decoys
  Default: 100
  

• optimization

  -optimization <Boolean>

  optimization option group
  

  -dfpmin_max_cycles <Integer>

  max cycles for dfpmin
  Default: 200
  

  -dfpmin_min_stepsize <Real>

  max cycles for dfpmin
  Default: 1e-8
  

• ufv

  -ufv <Boolean>

  ufv option group
  

  -left <Integer>

  left endpoint
  

  -right <Integer>

  right endpoint
  

  -ss <String>

  secondary structure string
  

  -aa_during_build <String>

  amino acid string during centroid build
  

  -aa_during_design_refine <String>

  amino acid string during design-refine
  

  -keep_junction_torsions <Boolean>

  when rebuilding loops, keep (approx) the original torsions at the junctions of the loop endpoints
  Default: false
  

  -ufv_loops <File>

  use this multiple loop file in place of specifying single loop options on command line
  

  -use_fullmer <Boolean>

  use full-mer fragments when building loop
  Default: false
  

  -centroid_loop_mover <String>

  the centroid loop mover to use
  Default: "RemodelLoopMover"
  

  -no_neighborhood_design <Boolean>

  only repack the neighborhood of the loop, don't design
  Default: false
  

  -dr_cycles <Integer>

  design-refine cycles
  Default: 3
  

  -centroid_sfx <String>

  filename of the centroid score function to use,
  

  -centroid_sfx_patch <String>

  filename of the centroid score function patch to use,
  

  -fullatom_sfx <String>

  filename of the full-atom score function to use
  

  -fullatom_sfx_patch <String>

  filename of the full-atom score function patch to use
  

• ufv:insert

  -insert <Boolean>

  insert option group
  

  -insert_pdb <File>

  pdb of insert structure
  

  -attached_pdb <File>

  pdb of structure in rigid body relationship with insert structure
  

  -connection_scheme <String>

  enforce type of insertion: choose either n2c or c2n
  

• rot_anl

  -rot_anl <Boolean>

  rot_anl option group
  

  -tag <String>

  nametag
  Default: "."
  

  -premin <Boolean>

  do all sc min and dump pdb
  Default: false
  

  -min <Boolean>

  do sc min
  Default: false
  

  -diff_to_min <Boolean>

  native pose is post-min
  Default: false
  

  -repack <Boolean>

  
  Default: false
  

  -rtmin <Boolean>

  
  Default: false
  

  -scmove <Boolean>

  
  Default: false
  

  -score_tol <Real>

  score filter for dump_pdb
  Default: 1.0
  

  -rmsd_tol <Real>

  rmsd filter for dump_pdb
  Default: 1.0
  

  -dump_pdb <Boolean>

  dump_pdb when pass thresh
  Default: false
  

  -nloop_scmove <Integer>

  base of scmover loop (total=nloop^n_chi)
  Default: 9
  

• lp

  -lp <Boolean>

  lp option group
  

  -Hpol <Boolean>

  lol
  Default: false
  

  -Haro <Boolean>

  lol
  Default: false
  

  -atomic_cutoff <Real>

  the atomic interaction cutoff for orb score
  Default: 15.0
  

  -verbose <Boolean>

  No description
  Default: false
  

  -bb_stats <Boolean>

  lol
  Default: false
  

  -sc_stats <Boolean>

  lol
  Default: false
  

  -orb_orb_stats <Boolean>

  lol
  Default: false