This vocabulary collects cmd-line flags used in Rosetta
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Click one of the letters above to advance the page to terms beginning with that letter.
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-abinitio::increase_cycles
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-abinitio:frags3
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-abinitio:frags9
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-abinitio:frags_large
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-abinitio:frags_small
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-abinitio:number_3mer_frags
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-abinitio:number_9mer_frags
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-abinitio:recover_low_in_stages
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-abinitio:rg_reweight
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-abinitio:rsd_wt_helix
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-abinitio:rsd_wt_loop
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-abinitio:skip_stages
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-abinitio:stage1_patch
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-abinitio:stage2_patch
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-abinitio:stage2_patch</td>
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-abinitio:stage3a_patch
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-abinitio:stage3b_patch
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-abinitio:stage3b_patch</td>
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-abinitio:stage4_patch
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-abinitio:stage4_patch</td>
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-constant_seed
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-constraint:threshold
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-constraints:cst_weight
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-database
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-fast_loops:window_accept_ratio
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-fold_cst:no_recover_low_at_constraint_switch
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-fold_cst:seq_sep_stages
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-fold_cst:skip_on_noviolation_in_stage1
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-in:centroid
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-in:file:centroid
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-in:file:fasta
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-in:file:frag3
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-in:file:frag9
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-in:file:fullatom
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-in:file:native
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-in:file:silent
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-in:fullatom
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-iterative:
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-iterative::auto_assign_scheme
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-iterative::cenpool_noesy_cst_weight
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-iterative::dcut
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-iterative::delay_noesy_reassign
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-iterative::initial_noe_auto_assign_csts
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-iterative::skip_redundant_constraints
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-iterative:accept_ratio
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-iterative:auto_assign_scheme
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-iterative:cen_score
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-iterative:cen_score_patch
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-iterative:cenpool_chemicalshift_weight
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-iterative:cenpool_noesy_cst_weight
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-iterative:centroid_before_quickrelax_weight
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-iterative:centroid_quickrelax
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-iterative:chemicalshift_column
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-iterative:dcut
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-iterative:delay_noesy_reassign
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-iterative:enumerate:broker
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-iterative:enumerate:skip_half
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-iterative:fa_score
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-iterative:fa_score_patch
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-iterative:fapool_chemicalshift_weight
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-iterative:flags_fullatom
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-iterative:force_topology_resampling
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-iterative:fullatom
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-iterative:fullatom_after_quickrelax_weight
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-iterative:initial_beta_topology
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-iterative:initial_noe_auto_assign_csts
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-iterative:max_nstruct
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-iterative:min_diversity
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-iterative:mix_frags
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-iterative:normalize:sampling
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-iterative:pool_size
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-iterative:recompute_beta_Naccept
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-iterative:rmsf_nstruct
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-iterative:safety_hatch_scorecut
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-iterative:skip_redundant_constraints
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-iterative:super_quick_relax_protocol
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-jran
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-jumps::increase_chainbreak
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-jumps:chainbreak_weight_stage1
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-jumps:chainbreak_weight_stage2
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-jumps:chainbreak_weight_stage3
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-jumps:chainbreak_weight_stage4
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-jumps:increase_chainbreak
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-jumps:overlap_chainbreak
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-jumps:ramp_chainbreaks
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-loops:alternative_closure_protocol
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-loops:idealize_after_loop_close
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-loops:idealize_before_loop_close
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-loops:non_ideal_loop_closing
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-noesy:in:peaks
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-noesy:in:resonances
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-nstruct
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-out:file:silent
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-out:file:silent_print_all_score_headers
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-out:nstruct
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-out:path
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-relax:default_repeats
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-relax:fast
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-relax:script
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-relax:thorough
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-residues:patch_selectors
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-run:dry_run
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-run:test_cycles
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-score:patch
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-score:weights
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-seed_offset
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