#You'll define your own database flag, of course
#-database /ifs1/home/smlewis/minirosetta_database

#useful for debugging
#-options:user
#-show_accessed_options
#-run:version

#input PDB
-s complex_readytail_final_nozn.pdb.gz

#ex flags give extra rotamers for packing; use_input_sc allows the pre-existing rotamer when packing (useful when paired with sidechain minimization)
#-ex1
#-ex2
-use_input_sc
#prevent design, keep the input sequence (use a resfile if you want design)
-packing:repack_only
#-resfile resfile

#minimizer type.  I don't know which is best
-run:min_type dfpmin_armijo_nonmonotone

#fragments if you want them; only 3mers are used.
#-in:file:frag3 complex_readytail_final_nozn_fragset3mer.gz #frags are too big to include in the demo

#local
#start of tail
-FloppyTail:flexible_start_resnum 180
#end of tail (assumed to be end of chain)
#-FloppyTail:flexible_stop_resnum 
#chain of tail
-FloppyTail:flexible_chain C
#used for preventing loss of compactness at centroid/fa switch; see documentation
-FloppyTail:short_tail:short_tail_off 0
-FloppyTail:short_tail:short_tail_fraction 1.0

#shear does nothing for extended tails; see documentation
-FloppyTail:shear_on .33333333333333333333

#turn this one OFF for other uses; activates publication-relevant metrics
-FloppyTail:publication true

#debugging
#-FloppyTail:perturb_show
#-FloppyTail:debug
#MC temperatures
#-FloppyTail:perturb_temp
#-FloppyTail:refine_temp

#frequency of full repacking; 10 used for test to fit in refine_cycles
#-FloppyTail:refine_repack_cycles 100
-FloppyTail:refine_repack_cycles 10

#low-end production numbers
#-FloppyTail:perturb_cycles 5000
#-FloppyTail:refine_cycles 3000
#-nstruct 5000

#runs in 26 seconds on my machine
-FloppyTail:perturb_cycles 100
-FloppyTail:refine_cycles 20
-nstruct 1