# 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

-abinitio
 #-relax	# do a relax refinement after each abinitio folding; default=false [Boolean]
  			# this does full-atom mode; omit this flag to do traditional (fast) centroid-based folding
 -fastrelax	# using a reduced number of cycles in the relax refinement protocol

-in
 -file
  -fasta 1ubi.fasta
  -frag3 fragments/aa1ubi_03_05.200_v1_3
  -frag9 fragments/aa1ubi_09_05.200_v1_3
   # 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
  #-native 1UBI.pdb 
   # you may optionally include the native structure if it is known
   # for benchmarking purposes. Use PDB format.
 -path
  -database  /programs/l/rosetta/3.1-x86_64/rosetta_database/
   # edit this path to point to your rosetta3 databases

-out
 #-path output	# path where PDB output files will be written to, default '.'
				# if you specify a directory name here, it must exist
 -nstruct 10	# the number of output decoys to produce - set this to a large number for good sampling
 #-pdb 			# output PDB files as well as silent.out, default=false [Boolean]
 -prefix bb		# the beginning part of output filenames, like the old -series code
  #-fullatom
   # low-resolution or "centroid" folding mode is the default; you must specify
   # fullatom output if you want to match -relax, above
 -file
  -silent folding_silent2.out	# name the "silent file" output; mult. structures in one file

# uncomment these commands to impose either centroid-based or full-atom constraints
#-constraints
 #-cst_file restraints
 #-cst_weight 1.0
 #-cst_fa_file fullatom.restraints
 #-cst_fa_weight 1.0


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

