# 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

-in
   -file
      -s 1ubi.pdb 
      # this is the input structure to be redesigned
   -path
      -database /programs/l/rosetta/3.1-x86_64/rosetta_database/
      # customize this to point to your installation directory

-resfile mutations.resfile
   # to specify what mutations are to be included in the design
-ignore_unrecognized_res
   # Do not abort if unknown residues are found in PDB file 
   # instead, ignore them. default='false'. [Boolean]
#-favor_native_res 0
   # a bonus energy added to the native res (default 0.5)
   # setting to zero will favor trivial modifications

-out
   -nstruct 10
   # this should be set to a large number for effective sampling
   -mute core.util.prof
   # reduces copious output, without overdoing as with -mute all
