// To be run from pce/casp5/t0159

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

Time

// readConformPDB robetta1.pdb
//     NameConform T0159.try11-robetta1
// readConformPDB decoys/T0159.try9-opt.pdb
//     NameConform T0159.try11-try9

// readConformPDB decoys/T0159-moved.pdb
//    NameConform T0159/try12-moved
    
ReadFragmentAlignment T0159-1amf-hand.vast.a2m

// ReadConformPDB decoys/T0159.try12-opt-scwrl.pdb
//     NameConform T0159.try14-try12

ReadConformPDB decoys/T0159.try13-opt-scwrl.pdb
    NameConform T0159.try15-try13
ReadConformPDB decoys/T0159.try11-opt.pdb
    NameConform T0159.try15-try11

ReportCost undertaker-try15.rdb

// ConformFromSeq replace // get a random conformation
//  NameConform T0159.rand

//   TryAllAlign shrink 0.4 min_keep_length 5 
//   TryAllAlign shrink 0.4 min_keep_length 5 cumulative
//  NameConform T0159.try15-al2
//  PrintConformPDB T0159.try15-al2.pdb edges
// 
//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0159.try15-al4
//  PrintConformPDB T0159.try15-al4.pdb edges

//   TryAllAlign shrink 0.3 min_keep_length 4 
//   TryAllAlign shrink 0.3 min_keep_length 4 cumulative
//  NameConform T0159.try15-al6
//  PrintConformPDB T0159.try15-al6.pdb edges

//  TryAllAlign shrink 0.1 min_keep_length 2 
//  TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//   NameConform T0159.try15-al8
//   PrintConformPDB T0159.try15-al8.pdb edges

//  TryAllAlign shrink 0.2 min_keep_length 3
//  TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//   NameConform T0159.try15-al10
//   PrintConformPDB T0159.try15-al10.pdb edges

//   TryAllAlign shrink 0. min_keep_length 1 
//   TryAllAlign shrink 0. min_keep_length 1 cumulative
//   NameConform T0159.try15-al12
//   PrintConformPDB T0159.try15-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.

Include T0159.t2k.undertaker-align.script 
ReadFragmentAlignment T0159.t2k-2track-undertaker.a2m

InFilePrefix 1ii5A/
Include read-alignments.under
InFilePrefix 1wdnA/
Include read-alignments.under
InFilePrefix 1gggB/
Include read-alignments.under
InFilePrefix 1sbp/
Include read-alignments.under
InFilePrefix 1ftkA/
Include read-alignments.under
InFilePrefix 1gr2A/
Include read-alignments.under
InFilePrefix 1iiwA/
Include read-alignments.under
InFilePrefix 1wod/
Include read-alignments.under
InFilePrefix 1amf/
Include read-alignments.under
InFilePrefix 1lst/
Include read-alignments.under
InFilePrefix 1ccwA/
Include read-alignments.under
InFilePrefix 1e5dA/
Include read-alignments.under
InFilePrefix 1kgsA/
Include read-alignments.under
InFilePrefix 1e6mA/
Include read-alignments.under
InFilePrefix 1cl1A/
Include read-alignments.under
InFilePrefix 1cl2A/
Include read-alignments.under

InfilePrefix
include subdomains.under


InFilePrefix 
ReadFragmentAlignment T0159.t2k.frag
ReadFragmentAlignment t0159-80-230/T0159.t2k.frag


OutFilePrefix 
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 0.2 \
	ClashingRotamer 0.5 \
	InsertFragment 9 \
	OneRotamer 0.2 \
	CrossOver 0 \
	CrossAndInsert 2 \
	TwoFragment 1 \
	InsertSpecificFragment 1 \
	ReduceBreak 5 \
	CloseGap 0.2 \
	OptSubtree 0.03 \
	JiggleSubtree 0.03 \
	ReduceClash 1 \
	InsertSSBond 0

NameConform T0159.try15
OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 5 \
	pdb scwrl_each use_all 
NameConform T0159.try15-opt
PrintConformPDB T0159.try15-opt.pdb edges

ScwrlConform
NameConform T0159-try15-opt-scwrl
PrintConformPDB T0159.try15-opt-scwrl.pdb 

CostConform
Time

quit