# by editing this file, you can customize the Rosetta run
# the format and content of this file is specified here:
# http://www.rosettacommons.org/manuals/rosetta3_user_guide/command_options.html
# note that here we format using indentation, alternately semicolons could have been used

-loops
 -input_pdb bPLAA.pdb
  # the starting "template" pdbfile should have the target sequence
 -loop_file bPLAA.loops
  # loopfile syntax is in the user manual
 -frag_sizes 9 3 1
  # default: 9 3 1
 -frag_files  fragments/aabPLAA09_05.200_v1_3 fragments/aabPLAA03_05.200_v1_3 none
   # these files contain structure fragments of length 3 and 9. They must be
   # generated anew for each sequence you want to fold,
   # either at robetta.bakerlab.org, or using the included scripts
 -build_initial 
   # Pre-build the loops to ensure missing atoms are accounted for, and no chainbreaks exist, before modeling
 -remodel quick_ccd
   # this uses cyclic coordinate descent (compare to kinematic loop closure)
 #-refine refine_ccd
 #-relax

-in
 -file
  -fullatom
 -path
  -database /programs/l/rosetta/3.1-x86_64/rosetta_database/
   # edit this path to point to your rosetta3 databases

-out
 -nstruct 20	# the number of output decoys to produce; use a large number for effective sampling
 -prefix aa		# the beginning part of output filenames, like the old -series code
 -file
  -fullatom	

-mute core.util.prof	# don't show timing info
#-no_prof_info_in_silentout		# or profiling info

