// To be run from pce/casp5/t0157

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0157.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0157.t2k.undertaker-align.script 
ReadFragmentAlignment T0157.t2k-2track-undertaker.a2m

InfilePrefix 1hjrA/
  Include read-alignments.under
InfilePrefix 1tplA/
  Include read-alignments.under
InfilePrefix 1dkuA/
  Include read-alignments.under
InfilePrefix 1kcfA/
  Include read-alignments.under
InfilePrefix 1dkrA/
  Include read-alignments.under
InfilePrefix 1j79A/
  Include read-alignments.under
InfilePrefix 1kczA/
  Include read-alignments.under

InfilePrefix

Time

ReadConformPDB decoys/T0157.try5-opt.pdb
    NameConformPDB T0157.try6-try5


ReportCost undertaker-try6.rdb

 TryAllAlign shrink 0.4 min_keep_length 5 
 TryAllAlign shrink 0.4 min_keep_length 5 cumulative
NameConform T0157.try6-al2
PrintConformPDB T0157.try6-al2.pdb edges

TryAllAlign shrink 0. min_keep_length 1 
TryAllAlign shrink 0. min_keep_length 1 cumulative
NameConform T0157.try6-al4
PrintConformPDB T0157.try6-al4.pdb edges

 TryAllAlign shrink 0.3 min_keep_length 4 
 TryAllAlign shrink 0.3 min_keep_length 4 cumulative
NameConform T0157.try6-al6
PrintConformPDB T0157.try6-al6.pdb edges

TryAllAlign shrink 0.1 min_keep_length 2 
TryAllAlign shrink 0.1 min_keep_length 2 cumulative
 NameConform T0157.try6-al8
 PrintConformPDB T0157.try6-al8.pdb edges

TryAllAlign shrink 0.2 min_keep_length 3
TryAllAlign shrink 0.2 min_keep_length 3 cumulative
 NameConform T0157.try6-al10
 PrintConformPDB T0157.try6-al10.pdb edges

 TryAllAlign shrink 0. min_keep_length 1 
 TryAllAlign shrink 0. min_keep_length 1 cumulative
 NameConform T0157.try6-al12
 PrintConformPDB T0157.try6-al12.pdb edges

CostConform
Time



// The following alignments are not as good as the ones tried above,
// so are not used in getting the starting point.

InFilePrefix 
ReadFragmentAlignment T0157.t2k.frag



OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 0.1 \
	ClashingRotamer 0.5 \
	InsertFragment 8 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 7 \
	ReduceBreak 1 \
	CloseGap 0.1 \
	OptSubtree 0.03 \
	JiggleSubtree 0.03 \
	ReduceClash 1 \
	InsertSSBond 0

NameConform T0157.try6
OptConform pool_size 40 num_gen 100 gen_size 200 super_iter 10 \
	pdb scwrl_each use_all
NameConform T0157.try6-opt
PrintConformPDB T0157.try6-opt.pdb edges

SCWRLconform
NameConform T0157.try6-opt-scwrl
PrintConformPDB T0157.try6-opt-scwrl.pdb
CostConform
Time

quit