Here is the loop file format. The columns are whitespace delimited. Only 1-3 are necessary.
column1 "LOOP": Literally the string LOOP, identifying this line as a loop In the future loop specification files may take other data. column2 "integer": Loop start residue number column3 "integer": Loop end residue number column4 "integer": Cut point residue number, >=startRes, <=endRes. Default or 0: let LoopRebuild choose cutpoint randomly. column5 "float": Skip rate. default - never skip column6 "boolean": Extend loop. Default false
LOOP 23 30 26 Loop from residues 23-30 with the cutpoint at 26.
-nstruct number of outputs. [Integer] -database Path to rosetta3 databases. [PathVector] -in:file:fullatom Enable full-atom input from PDB. [Boolean] -loops::input_pdb Path/name of input pdb file. Note that this is NOT -s/-l like normal. [File] -loops:loop_file Path/name of loop definition file. default "loop_file". [File] -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]
Rosetta can figure out secondary structure from phi/psi, but if you know it already (and/or trust your assignment more than Rosetta's) you can use these flags:
-in::file::psipred_ss2 For psipred_ss2 (pass path to file). [File] -in::file::dssp For dssp (pass path to dssp file). [File]
A series of string options control what sorts of loop modeling you get. The executable contains many different loop modeling modes, you use string selections to tell it which paths to take. These options are listed in the order that they take effect (the order that the steps happen in the program).
-loops::build_initial Pre-build the loops to ensure missing atoms are accounted for, and no chainbreaks exist, before modeling. [Boolean] -loops::remodel Legal values: 'no','perturb_ccd','quick_ccd','quick_ccd_moves','old_loop_relax'. default='quick_ccd'.[String] This option controls the centroid-stage loop remodeling (where large perturbations are attempted). -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::idealize_before_relax Idealize the structure after refinement, sometimes useful if you want a final relax step.[boolean] -loops::relax Legal values: 'no','fastrelax','shortrelax','fullrelax' [String] Controls whether a full-structure relax occurs after loop modeling. Defaults to "no".
The specifically important terms:
rama Ramachandran energy (phi and psi dihedrals in the backbone) omega omega dihedral in the backbone chainbreak measures whether the loop was successfully closed.