// To be run from pce/casp5/t0146

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0146.t2k.undertaker-align.script 
ReadFragmentAlignment T0146.t2k-2track-undertaker.a2m

//include read-subdomain.under

Time

// ReadConformPDB robetta1.pdb.gz
//   Nameconform T0146.try3-robetta1
// ReadConformPDB robetta2.pdb.gz
//   Nameconform T0146.try3-robetta2
// ReadConformPDB robetta3.pdb.gz
//   Nameconform T0146.try3-robetta3
// ReadConformPDB robetta4.pdb.gz
//   Nameconform T0146.try3-robetta4
// ReadConformPDB robetta5.pdb.gz
//   Nameconform T0146.try3-robetta5

// ReadConformPDB decoys/T0146.try4-opt-scwrl.pdb
//    NameConform T0146.try5-try4
// ReadConformPDB decoys/T0146.try3-opt.pdb
//    NameConform T0146.try5-try3

// ReadConformPDB robetta1.pdb.gz
//   Nameconform T0146.try6-robetta1
// ReadConformPDB robetta2.pdb.gz
//   Nameconform T0146.try6-robetta2
// ReadConformPDB robetta3.pdb.gz
//   Nameconform T0146.try6-robetta3
// ReadConformPDB robetta4.pdb.gz
//   Nameconform T0146.try6-robetta4
// ReadConformPDB robetta5.pdb.gz
//   Nameconform T0146.try6-robetta5

//ReadConformPDB decoys/T0146.try4-opt.pdb
// NameConform T0146.try17-try4
//ReadConformPDB decoys/T0146.try6-opt-scwrl.pdb
//   NameConform T0146.try17-try6
//ReadConformPDB decoys/T0146.try7-opt-scwrl.pdb
//   NameConform T0146.try17-try7
//ReadConformPDB decoys/T0146.try8-opt-scwrl.pdb
//   NameConform T0146.try17-try8


// ReadConformPDB decoys/T0146.try16-try15-moved.pdb
//   NameConform T0146.try17-try16-moved
  
// ReadConformPDB decoys/T0146-robetta-moved.pdb
//    NameConform T0146.try17-T0146-robetta-moved.pdb
	
// ReadConformPDB decoys/T0146.try17-opt.pdb
//   NameConform T0146.try18-try17


ReadConformPDB decoys/T0146.try3-robetta2.1.60.pdb
  NameConform T0146.try28-model1

  
ReportCost undertaker-try28.rdb

//  ConformFromSeq	replace // get a random conformation, removing all-zero one
//  NameConform T0146.rand

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
//  NameConform T0146.try28-al2
//  PrintConformPDB T0146.try28-al2.pdb edges
 
//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0146.try28-al4
//  PrintConformPDB T0146.try28-al4.pdb edges
 
//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
//  NameConform T0146.try28-al6
//  PrintConformPDB T0146.try28-al6.pdb edges
 
//  TryAllAlign shrink 0.1 min_keep_length 2 
//  TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0146.try28-al8
//  PrintConformPDB T0146.try28-al8.pdb edges
 
//  TryAllAlign shrink 0.2 min_keep_length 3
//  TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0146.try28-al10
//  PrintConformPDB T0146.try28-al10.pdb edges
 
//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0146.try28-al12
//  PrintConformPDB T0146.try28-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 T0146.t2k.frag
ReadFragmentAlignment t0146-1-80/T0146.t2k.frag
ReadFragmentAlignment t0146-1-180/T0146.t2k.frag
ReadFragmentAlignment t0146-120-220/T0146.t2k.frag
ReadFragmentAlignment t0146-180-325/T0146.t2k.frag


OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time


InitMethodProbs InsertAlignment 0.3 \
	ClashingRotamer 0.5 \
	InsertFragment 10 \
	CrossAndInsert 2 \
	CrossOver 0 \
	TwoFragment 1 \
	InsertSpecificFragment 5 \
	ReduceBreak 0.5 \
	CloseGap 0.1 \
	OptSubtree 0.03 \
	JiggleSubtree 0.03 \
	ReduceConstraint 1 \
	ReduceClash 1 \
	InsertSSBond 0

NameConform T0146.try28
OptConform pool_size 70 num_gen 80 gen_size 180 super_iter 40 \
	pdb scwrl_each use_all 
NameConform T0146.try28-opt
PrintConformPDB T0146.try28-opt.pdb edges

SCWRLconform
NameConform T0146.try28-opt-scwrl
PrintConformPDB T0146.try28-opt-scwrl.pdb
CostConform
Time

quit