# notes:
This protocol can be extended by increasing the quantities at any stage.  Particluarly: number of input loops, length of refinement, number of permuted output.

# pick loops using the script:
/users/jack/single_alignment/pickLoops.pl
# it calls nnmake, given a template, sequence, profile  and zones file 
# (all available in /data/robetta/casp6/)

# close loops:
~/Loops/dunbrack/rosetta++/rosetta.gcc 00 t000 _ -screen -loops -dunbrack_close -s t000_.pdb -fast > 00.log

# take all loops that have 0.0 bump score
awk '$6==0.0' output/t000_-1ml8A_.0001.base.loops_all.screened > test.loops.filtered

# put on short dummy loops:
~/Loops/dunbrack/rosetta++/rosetta.gcc 01 t000 _ -loops -loop_library loops.filtered -permute -s t000_.pdb -fast -nstruct 1 > 01.log

cp output/01t000__0001.pdb ./dummy.pdb

# make long loop library, # fold long loops  ?
#awk '$1>=17 ' t000_.loops.filtered > dummy.long
#~/Loops/screen_fa/rosetta.gcc 03 t000 _ -s dummy -loops -loop_library long -fast > 03.log

# repack input - extra chis?
~/Loops/dunbrack/rosetta++/rosetta.gcc -fa_output -nstruct 1 -score -s dummy.pdb -fa_lj_rep_slope lowres > repack.log

cp output/dummy_0001.pdb ./dummy3.pdb

# fa refine short loops
awk '$1<17' t000_.loops.filtered > dummy3.short

~/Loops/screen_fa/rosetta.gcc 07 t000 _ -loops -loop_library short -screen -s dummy3.pdb -fa_input -fa_lj_rep_slope lowres > & 07.log & tail -f 07.log

# pick 5 best scoring refined loops

sort -k6n output/dummy3.short.screened | awk '{count[$2]++; if (count[$2] <= 5) {print $0 }}' | sort -k2n > dummy3.short.best5

# permute to make 3
~/Loops/dunbrack/rosetta++/rosetta.gcc 08 t000 _ -loops -loop_library short.best5 -permute -s dummy3.pdb -fast -nstruct 3 -no_filter > 08.log & tail -f 08.log

# repack and fa_refine those 3?
'ls' -1 output/08*pdb > 08.list

#~/Loops/dunbrack/rosetta++/rosetta.gcc -fa_output -nstruct 1 -score -l 08.list -fa_lj_rep_slope lowres -scorefile repack -scorefxn 12 > repack.log

~/Loops/dunbrack/rosetta++/rosetta.gcc 10 t000 _ -loops -loop_library short.best5 -fa_refine -l repack.list -no_filter > 10.log & tail -f 10.log

# repack
~/Loops/dunbrack/rosetta++/rosetta.gcc -fa_output -nstruct 1 -score -s output/0908dummy3_0001_0001.pdb -ex1 -ex2 -ex1aro -fa_lj_rep_slope lowres > repack2.log

# issues
1) When to model long loops
2) Using trimmed region in during relaxation
3) Making larger loop libraries