Rosetta 3.1 Release Manual |
-lopps:input_pdb Template pdb file. default='input_pdb' [File] -loops:loop_file Loop definition file. default='loop_file' [File] -loops:mm_loop_file Loop definition file. default='loop_file' [File] -loops:fix_natsc Fix sidechains in template region in loop modeling. Default='false' [Boolean] -loops:refine_only Perform full atom refinement only on loops. Default='false' [Boolean] -loops:fa_input Input structures are in full atom format. Default='false' [Boolean] -loops:fast Reduce number of simulation cycles in loop modeling. Default='false' [Boolean] -loops:frag_sizes (non-kic modes only) Length of fragments to be used in loop modeling (in other words, number of amino acids/residues for each segment. For each type of fragment). defaults to 9 3 1 [IntegerVector] -loops:frag_files (non-kic modes only) Path/Name of fragment libraries files, defaults to frag9 frag3 frag1. [FileVector] -loops:build_initial Preceed loopmodelling with a initial round of just removing the missing densities and building simple loop. Default = 'false'. [Boolean] -loops:extended Force extended on loops, independent of loop input file. Default='false' [Boolean] -loops:idealize_before_relax Idealize the structure before going into fa relax. Default='false' [Boolean] -loops:select_best_loop_from Keep building loops until N and choose best (by score). Default='1' [Integer] -loops:build_attempts Build attempts per growth attempt. Default='3' [Integer]
-loops:neighbor_dist Distance in angstroms to optimize side-chains near segment moved by KIC. Default='10.0' [Real] -loops:vicinity_sampling Sample non-pivot torsions within a vicinity of their input values. Default='false' [Boolean] -loops:vicinity_degree Number of degrees to deviate from (current) non-pivot torsions. Default='1.0' [Real] -loops:kic_max_seglen Maximum number residues in a KIC move segment. Default='12' [Integer] -loops:remodel_init_temp Initial temperature for simulated annealing for perturb_kic -loops:remodel_final_temp Final temperature for simulated annealing for perturb_kic -loops:refine_init_temp Initial temperature for simulated annealing for refine_kic -loops:refine_final_temp Final temperature for simulated annealing for refine_kic
-loops:grow_attempts Total loop growth attempts. Default='7' [Integer] -loops:random_grow_loops_by Randomly grow loops by up to this number of residues on either side. Default='0.0' [Real] -loops:accept_aborted_loops Accept aborted loops. Default='false' [Boolean] -loops:strict_loops Do not allow growing of loops. Default='false' [Boolean]
-loops:build_specific_loops Numbers of the loops to be built. [IntegerVector] -loops:random_order Build in random order. Default='false' [Boolean] -loops:build_all_loops Build all loops(no skip). Default='false' [Boolean] -loops:combine_rate Combine successive loops at this rate. Default='0.0' [Real] -loops:
-loops:remodel Legal values: 'no','perturb_ccd','perturb_kic'. This option controls the centroid-stage loop remodeling (where large perturbations are attempted). Default = 'quick_ccd' [String] -loops:intermedrelax Currently not used; Eventually may provide for a full-pose relax between centroid and fullatom modeling. default = 'no' [String] -loops:refine Legal values: 'no','refine_ccd','refine_kic'. This option controls the fullatom refinement stage of loop. modeling. Default = 'no' [String] -loops:relax Legal values: 'no','fastrelax','shortrelax','fullrelax' [String] Controls whether a full-structure relax occurs after loop modeling. Defaults to "no".