// To be run from pce/casp5/t0141

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


// The following alignments are believed to be good:
InFilePrefix 

InFilePrefix 
Time


OutFilePrefix decoys/

InFilePrefix 

ReadTemplateAtoms Template.atoms


InFilePrefix 
Include T0141.undertaker-align.script 
ReadFragmentAlignment T0141.t2k-2track-undertaker.a2m

InFilePrefix 1aroL/
    include read-alignments.under
InFilePrefix 1lba/
    include read-alignments.under
InFilePrefix 


Time

// ReadConformPDB decoys/T0141.try6-opt-scwrl.pdb
// NameConform T0141.try7-try6

// ReadConformPDB decoys/T0141.try6-opt-scwrl.pdb
// NameConform T0141.try8-try6
// ReadConformPDB decoys/T0141.try7-opt-scwrl.pdb
// NameConform T0141.try8-try7

// ReadConformPDB decoys/T0141.try8-opt.pdb
// NameConform T0141.try9-try8

// ReadConformPDB decoys/T0141-moved.pdb
// NameConform T0141.try10-moved

// ReadConformPDB decoys/T0141.try10-opt-scwrl.pdb
// NameConform T0141.try11-try10

// ReadConformPDB decoys/T0141.try11-opt.pdb
// NameConform T0141.try12-try11

// ReadConformPDB decoys/T0141-moved2.pdb
// NameConform T0141.try13

// ReadConformPDB decoys/T0141.cut-and-paste.pdb
// NameConform T0141.try14

// ReadConformPDB decoys/T0141.try14-opt.pdb
// NameConform T0141.try15-try14

// ReadConformPDB decoys/T0141.try14-opt.pdb
// NameConform T0141.try16-try14
// ReadConformPDB decoys/T0141.try15-opt-scwrl.pdb
// NameConform T0141.try16-try15-s
// ReadConformPDB decoys/T0141.try15.9.90.pdb
// NameConform T0141.try16-try15-9
// ReadConformPDB decoys/T0141.try15.8.90.pdb
// NameConform T0141.try16-try15-8
// ReadConformPDB decoys/T0141.try15.9.90.pdb
// NameConform T0141.try16-try15-9

// ReadConformPDB decoys/T0141.try16-opt.pdb
//     NameConform T0141.try17-try16
// ReadConformPDB decoys/T0141.try16-opt-scwrl.pdb
//     NameConform T0141.try17-try16-s
// ReadConformPDB decoys/T0141.try16-scwrl.10.100.pdb
//     NameConform T0141.try17-try16-10
// ReadConformPDB decoys/T0141.try16.2.100.pdb
//     NameConform T0141.try17-try16-2

// ReadConformPDB decoys/T0141.try17-opt-scwrl.pdb
//      NameConform T0141.try18-try17-s
// ReadConformPDB decoys/T0141.try17.1.50.pdb
//      NameConform T0141.try18-try17-1
// ReadConformPDB decoys/T0141.try17.4.50.pdb
//      NameConform T0141.try18-try17-4
// ReadConformPDB decoys/T0141.try17.3.50.pdb
//      NameConform T0141.try18-try17-3
// ReadConformPDB decoys/T0141.try17.5.50.pdb
//      NameConform T0141.try18-try17-5
// ReadConformPDB decoys/T0141.try17.2.50.pdb
//      NameConform T0141.try18-try17-2

// ReadConformPDB decoys/T0141.try15.9.90.pdb
//      NameConform T0141.try19-try15-9
// ReadConformPDB decoys/T0141.try18.1.50.pdb
//      NameConform T0141.try19-try18-1
// ReadConformPDB decoys/T0141.try16.7.100.pdb
//      NameConform T0141.try19-try16-7
// ReadConformPDB decoys/T0141.try18.3.50.pdb
//      NameConform T0141.try19-try18-3
// ReadConformPDB decoys/T0141.try18.3.50.pdb
//      NameConform T0141.try19-try18-3
// ReadConformPDB decoys/T0141.try17-opt-scwrl.pdb
//      NameConform T0141.try19-try17-s

ReadConformPDB decoys/T0141.try17-opt-scwrl.pdb
      NameConform T0141.try20-try17-s
ReadConformPDB decoys/T0141.try18.3.50.pdb
    NameConform T0141/try20-try18-3
ReadConformPDB decoys/T0141.try19-opt-scwrl.pdb
    NameConform T0141/try20-try19-s
ReadConformPDB decoys/T0141.try19-try16-7.1.50.pdb
    NameConform T0141/try20-try19-1
ReadConformPDB decoys/T0141.try19-try16-7.5.50.pdb
    NameConform T0141/try20-try19-5
    
ReportCost undertaker-try20.rdb


// ConformFromSeq replace // get a random conformation, removing all-zero one
// NameConform T0141.rand
// Time

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0141.try20-al2
// PrintConformPDB T0141.try20-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0141.try20-al4
// PrintConformPDB T0141.try20-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0141.try20-al6
// PrintConformPDB T0141.try20-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0141.try20-al8
//  PrintConformPDB T0141.try20-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0141.try20-al10
//  PrintConformPDB T0141.try20-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0141.try20-al12
//  PrintConformPDB T0141.try20-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 T0141.t2k.frag

OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 0 \
	ClashingRotamer 4 \
	InsertFragment 20 \
	CrossAndInsert 1 \
	CrossOver 0 \
	TwoFragment 1 \
	InsertSpecificFragment 5 \
	ReduceBreak 1 \
	CloseGap 0.2 \
	OptSubtree 0.03 \
	JiggleSubtree 0.03 \
	Reduceclash 2 \
	InsertSSBond 0

NameConform T0141.try20
OptConform pool_size 40 num_gen 100 gen_size 200 super_iter 10 pdb \
	use_all scwrl_each
NameConform T0141.try20-opt
PrintConformPDB T0141.try20-opt.pdb edges

SCWRLConform
NameConform T0141.try20-opt-scwrl
PrintConformPDB T0141.try20-opt-scwrl.pdb edges

CostConform
Time

quit