| Rosetta 3.2.1 Release Manual |
bin/loopmodel.*. The main ccd loop movers are perturb_ccd which exists in src/protocols/loops/LoopMover_CCD.cc and quick_ccd which exists in LoopMover_QuickCCD.cc. Both protocols generate loops by assembling them from fragments by Monte Carlo sampling and uses CCD to close the loops. The most commonly used method for fragment-based loop modeling is currently quick_ccd. Option -loops:remodel quick_ccd_moves is no longer in widespread use, but exists for backward compatibility.A usage example that remodels 10 and 5-residue loops is in the loop_modeling integration test, found here:
test/integration/tests/loop_modeling
Wang C, Bradley P, Baker D (2007). Protein-protein docking with backbone flexibility. J. Mol. Biol. 373, 503.
The original CCD algorithm is described in
Canutescu A, Dunbrack R., Jr (2003). Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12, 963.
The centroid stage of loop-modeling generates loops by performing fragment insertions using Monte Carlo sampling, a score to reward closed chains, and CCD is used to close the loop at the end of the simulation. As the fragments are necessary for the sampling these have to be generated by fragment picker ( c.f. fragment picker documentation) or downloaded from the Robetta web-server. Fragments are loaded with the following options:
-loops:frag_sizes (defines the number of residues in each fragment file) -loops:frag_files (defines the name of each fragment file)
An alternative option exists, -loops:vall_file, that lets the user pick fragments on the fly using a sequence-identity based scoring method for selecting fragments. In most cases, this option will lead to less suboptimal results for a given input sequence, as the fragments picked will not take advantage of sequence profile and secondary structure information.
-loops:loop_file
and shared across all loop modeling protocols. For each loop to be modeled, include the following on one line:
column1 "LOOP": The loop file identify tag column2 "integer": Loop start residue number column3 "integer": Loop end residue number column4 "integer": Cut point residue number, >=startRes, <=endRes. default - let the loop modeling code choose cutpoint column5 "float": Skip rate. default - never skip column6 "boolean": Extend loop. Default false
An example loop definition file can be found at test/integration/tests/kinematic_looprelax/input/4fxn.loop, which looks like this:
LOOP 88 95 92 0 1
Loop modeling control: 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.
-loops:input_pdb
input pdb file that loop modelling is done on (-in:file:s is not supported)
default='input_pdb'
-loops:remodel
legal=['no', 'perturb_ccd', 'perturb_kic', 'quick_ccd',
'quick_ccd_moves', 'old_loop_relax', 'sdwindow']
Centroid version of loopmodeling.
peturb_kic: for the kic loopclosure
perturb_ccd: original fragment/ccd loop closure method
quick_ccd: faster fragment/ccd loop closure method
older unused methods: quick_ccd_moves, old_loop_relax, sdwindow
The preferred method CCD looprelax is quick_ccd
-loops:refine
legal=['no','refine_ccd','refine_kic']
Method for performing full-atom refinement on loops.
The preferred method for full-atom refinment is refine_kic
-loops:loop_file
Loop definition file(s). When multiple files are given a *random* one will be picked
each time when this parameter is requested.
-loops:vall_file vall database file for picking crude fragments on the fly without inputting pregenerated fragments default='vall_file' -loops:frag_sizes lengths of fragments to be used in loop modeling default=['9','3','1'] -loops:frag_files fragment libraries files default=['frag9', 'frag3', 'frag1']
-loops:relax legal=['no','fastrelax','shortrelax','fullrelax','seqrelax','minirelax'] does a relax on the structure - minimization in the torsion space default = 'no' -loops:extended force extended on loops (phi-psi angles set to 180 degrees), independent of loop input file legal=['true','false'] default='false'
-nstruct number of outputs. [Integer] -database Path to Rosetta databases. [PathVector]
-loopsremodel quick_ccd -loopsrefine refine_kic -loopsrelax fastrelax -relaxfastrelax_repeats 8 -loopsextended and to generate at least 1000 models using -nstruct 1000.quick_ccd can also remodel termini. To do this set the cutpoint in the loops file to be equal to the last residue in the chain. For example for a 80 residue protein, if you want to remodel the first 10 residues the loop file would have 1 10 10 0 0
quick_ccd does not require constraints, but using constraints from homologs or experimental data can produce more accurate results. Output consists of a pdb and a scorefile. The job concludes with the following command:
protocols.looprelax: ===
protocols::checkpoint: Deleting checkpoints of Loopbuild
1.5.9