-run:protocol threading

-in:file:fasta ./inputs/query.fasta
-cm:aln_format grishin
-in:file:alignment ./inputs/query.grishin

-in:file:psipred_ss2 ./inputs/t000_.psipred_ss2
-in:file:fullatom
-nstruct 200
-in:file:template_pdb ./inputs/2XAUA.PDB_A.pdb
-database /cluster/apps/fred/rosetta/main/database

#-loops:loop_file ./inputs/query.loops
-loops:frag_sizes 9 3 1
-loops:frag_files ./inputs/t001_.200.9mers ./inputs/t001_.200.3mers none
-loops:extended
-loops:build_initial
-loops:remodel quick_ccd
-loops:refine refine_ccd
-random_grow_loops_by 4 
-select_best_loop_from 1 

#-idealize_after_loop_close
#-cm:min_loop_size 4


-out:file:fullatom 
-out:output
-out:file:silent ./query_silent.out
-out:file:silent_struct_type binary

#-out:file:scorefile ./silent/query_silent.scr # 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
#-jd2:mpi_timeout_factor 0.0
#-out:level 400