-run:protocol threading # run the rosetta threading, loopbuilding, and refinement protocol
-in:file:alignment $HOME/Scratch/20141110_HC_minirosetta/input/C226S_4KMT_HC.aln # path to alignment file
-cm:aln_format general # format of alignment file
-frag3 $HOME/Scratch/20141110_HC_minirosetta/input/aaC226S_HC03_05.200_v1_3 # path in 3mer fragment file
-frag9 $HOME/Scratch/20141110_HC_minirosetta/input/aaC226S_HC09_05.200_v1_3 # path to 9mer fragment file
-in:file:fasta $HOME/Scratch/20141110_HC_minirosetta/input/C226S_HC.fasta # path to target fasta file
-in:file:fullatom # we have fullatom format for the input template
-loops:frag_sizes 9 3 1 # which size fragments are you using?
-loops:frag_files $HOME/Scratch/20141110_HC_minirosetta/input/aaC226S_HC09_05.200_v1_3 $HOME/Scratch/20141110_HC_minirosetta/input/aaC226S_HC03_05.200_v1_3 none	# paths to 9mer file, 3mer file, and say "none" for the 1mer file
-in:file:psipred_ss2 $HOME/Scratch/20141110_HC_minirosetta/input/C226S_HC.psipred_ss2 # path to psipred secondary structure prediction file
-in:file:fullatom 
#-out:nstruct 10000 # number of structures you want to build.  Should build at least 1000, but 10,000 would be better
-out:nstruct 1
-in:file:template_pdb $HOME/Scratch/20141110_HC_minirosetta/input/4KMT_HC_FullAtom.pdb # path to template pdb
-loops:extended # Force extended on loops, independent of loop input file
-loops:build_initial # Precede loop-modeling with an initial round of just removing the missing densities and building simple loops
-loops:remodel quick_ccd # closing loops by quick_ccd
-loops:refine refine_ccd # small movements to remodel loop
-silent_decoytime # Add time since the last structure was written to score line
-random_grow_loops_by 4 # randomly grow loops by up to this number of residues on either side.
-select_best_loop_from 1 # Keep building loops until N and choose best (by score)
-out:file:fullatom # output in fullatom mode
-out:output
#-out:file:silent threaded_model.out # silent file stores internal coordinates of the PDB
#-out:file:silent_struct_type binary # output the silent file in binary format
-out:pdb
-out:file:scorefile threaded_model.fasc # output a table of Rosetta scores
-run:constant_seed # Use a constant seed (1111111 unless specified)
-run:jran 1111111 # this is good for testing since you should always get the same result
-overwrite # overwrite any already-existing results having the same name