// To be run from pce/casp5/t0132

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0132-rand
Time


ReadTemplateAtoms Template.atoms

InFilePrefix 1bvqA/
Include read-alignments.under
InFilePrefix 1lo7A/
Include read-alignments.under
InFilePrefix 1c8uA/
Include read-alignments.under

InFilePrefix selected/1bvqA/
Include read-alignments.under
InFilePrefix selected/1lo7A/
Include read-alignments.under
InFilePrefix selected/1c8uA/
Include read-alignments.under

InFilePrefix 
Include T0132.t2k.undertaker-align.script 

ReadFragmentAlignment T0132.t2k-2track-undertaker.a2m

// ReadConformPDB decoys/T0132.try14-opt.pdb
// NameConform T0132.try17-try14
// ReadConformPDB decoys/T0132.try8.6.30.pdb
// NameConform T0132.try17-try8

// ReadConformPDB decoys/T0132.try15-opt-scwrl.pdb
// NameConform T0132.try17-try15
// ReadConformPDB decoys/T0132.try15-al6.18.25.pdb
// NameConform T0132.try17-try15-18

// ReadConformPDB decoys/T0132.try16-opt.pdb
// NameConform T0132.try17-try16

// ReadConformPDB decoys/T0132.try18-opt-scwrl.pdb
// NameConform T0132.try22-try18
// ReadConformPDB decoys/T0132.try19-opt-scwrl.pdb
// NameConform T0132.try22-try19
// ReadConformPDB decoys/T0132.try19.6.20.pdb
// NameConform T0132.try22-try19-6
// ReadConformPDB decoys/T0132.try20-opt-scwrl.pdb
// NameConform T0132.try22-try20
// ReadConformPDB decoys/T0132.try21-opt.pdb
// NameConform T0132.try22-try21
// ReadConformPDB decoys/T0132.try21-opt-scwrl.pdb
// NameConform T0132.try22-try21-scwrl

// ReadConformPDB decoys/T0132.try22-opt.pdb
// NameConform T0132.try23-try22

// ReadConformPDB decoys/T0132.try23-opt-scwrl.pdb
// NameConform T0132.try24-try23

// ReadConformPDB decoys/T0132.try24-opt-scwrl.pdb
// NameConform T0132.try25-try24

// ReadConformPDB decoys/T0132.try25.9.40.pdb
// NameConform T0132.try26-try25-9

// ReadConformPDB decoys/T0132.try25.4.40.pdb
// NameConform T0132.try26-try25-4

ReadConformPDB decoys/T0132.try26-opt-scwrl.pdb
NameConform T0132.try27-try26

Time

ReportCost undertaker.try27.rdb

// TryAllAlign shrink 0.4 min_keep_length 5 
// TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0132.try27-al2
// PrintConformPDB T0132.try27-al2.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
// NameConform T0132.try27-al4
// PrintConformPDB T0132.try27-al4.pdb edges

// TryAllAlign shrink 0.3 min_keep_length 4 
// TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0132.try27-al6
// PrintConformPDB T0132.try27-al6.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0132.try27-al8
// PrintConformPDB T0132.try27-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
// NameConform T0132.try27-al10
// PrintConformPDB T0132.try27-al10.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0132.try27-al12
// PrintConformPDB T0132.try27-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.

ReadFragmentAlignment T0132.t2k.frag
InFilePrefix 

// OutFilePrefix
// PrintTemplateAtoms Template.atoms
// OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 0.5 \
	ClashingRotamer 0.5 \
	InsertFragment 1 \
	CrossAndInsert 2 \
	TwoFragment 1 \
	InsertSpecificFragment 0.5 \
	ReduceBreak 5 \
	CloseGap 1 \
	ReduceClash 1 \
	ReduceConstraint 2 \
	JiggleSubTree 0.2 \
	OptSubtree 0.2 \
	InsertSSBond 0 \
	ImproveSSBond 0

// NameConform T0132.try27
OptConform pool_size 60 num_gen 30 gen_size 180 super_iter 10 \
	pdb scwrl_each use_all
NameConform T0132.try27-opt
PrintConformPDB T0132.try27-opt.pdb edges
SCWRLConform
NameConform T0132.try27-opt-scwrl
PrintConformPDB T0132.try27-opt-scwrl.pdb

CostConform
Time

quit