Loop Modeling Options

Here is a list of loop modeling options

General Instruction

-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			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			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]

Options affecting growing/combining of loops

-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]

Options affection choice of loops

-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]

Subprotocol Components

-loops:remodel				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'.
					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".

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