# by editing this file, you can customize the Rosetta run
# the format and content of this flags file is specified here:
# http://www.rosettacommons.org/manuals/rosetta3.1_user_guide
# note that here we format using indentation, alternatively semicolons could have been used

-cluster
   -radius 7
    # default clustering radius is 3A
    # fiddling with the radius is the simplest way to vary the clustering
   #-input_score_filter 100
    # exclude structures above a given energy (in Rosetta Energy Units)
   #-limit_clusters 5
    # only retain largest N clusters
   #-remove_highest_energy_member
    # remove putative outlier from each cluster

-in
 -file
  -silent folding.silent.out
  -fullatom
   # the clustering executable accepts a set of pdbfiles, (-s *pdb)
   # a file containing a list of pdbfiles, or
   # a silentfile containing multiple structures
  #-native 1ubi.pdb 
   # you may optionally include the native structure if it is known
   # for benchmarking purposes. It will calculate CaRMSD from native.
 -path
  -database /programs/l/rosetta/3.1-x86_64/rosetta_database/
   # edit this path to point to your rosetta3 databases

-out
 #-prefix aa
 #
 #-path output	# path where PDB output files will be written to, default '.'
				# if you specify a directory name here, it must exist
 #-nooutput		# suppress output of pdbfile structures

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

