// To be run from pce/casp5/t0144

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time



OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0144.rand
Time



InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0144.undertaker-align.script 
ReadFragmentAlignment T0144.t2k-2track-undertaker.a2m

InFilePrefix 1dywA/
    include read-alignments.under
InFilePrefix 1awqA/
    include read-alignments.under
InFilePrefix 2cpl/
    include read-alignments.under
InFilePrefix 1cwoA/
    include read-alignments.under
InFilePrefix 1ihgA/
    include read-alignments.under
InFilePrefix 1awsA/
    include read-alignments.under
InFilePrefix 2rmcA/
    include read-alignments.under
InFilePrefix 1a58/
    include read-alignments.under

InFilePrefix 


Time

InFilePrefix decoys/
// ReadConformPDB T0144.try1-opt.pdb
//  NameConform T0144.try7-try1
// ReadConformPDB T0144.try2-opt.pdb
//  NameConform T0144.try7-try2
// ReadConformPDB T0144.try3-opt.pdb
//  NameConform T0144.try7-try3
// ReadConformPDB T0144.try4-opt.pdb
//  NameConform T0144.try7-try4
// ReadConformPDB T0144.try5-opt.pdb
//  NameConform T0144.try7-try5
// ReadConformPDB T0144.try5-try4.9.20.pdb
//  NameConform T0144.try7-try5-try4.9.20
// ReadConformPDB T0144.try6-opt.pdb
//  NameConform T0144.try7-try6

// ReadConformPDB T0144.try8-opt.pdb
//   NameConform T0144.try10-try8
// ReadConformPDB T0144.try9-opt.pdb
//   NameConform T0144.try10-try9


// ReadConformPDB T0144.try10-opt.pdb
//  NameConform T0144.try11-try10


ReadConformPDB T0144.try11-opt.pdb
  NameConform T0144.try12-try11
ReadConformPDB T0144.try11.5.80.pdb
  NameConform T0144.try12-try11-5
ReadConformPDB T0144.try11.17.80.pdb
  NameConform T0144.try12-try11-17
ReadConformPDB T0144.try11.16.80.pdb
  NameConform T0144.try12-try11-16

InFilePrefix

ReportCost undertaker-try12.rdb


//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0144.try12-al2
// PrintConformPDB T0144.try12-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0144.try12-al4
// PrintConformPDB T0144.try12-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0144.try12-al6
// PrintConformPDB T0144.try12-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0144.try12-al8
//  PrintConformPDB T0144.try12-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0144.try12-al10
//  PrintConformPDB T0144.try12-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0144.try12-al12
//  PrintConformPDB T0144.try12-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 T0144.t2k.frag
InFilePrefix 

Time



InitMethodProbs InsertAlignment 0.1 \
	ClashingRotamer 0.5 \
	InsertFragment 9 \
	CrossAndInsert 2 \
	CrossOver 0 \
	TwoFragment 20 \
	InsertSpecificFragment 5 \
	ReduceBreak 1 \
	CloseGap 0.3 \
	OptSubtree 0.03 \
	JiggleSubtree 0.03 \
	ReduceClash 2 \
	InsertSSBond 0 \
	ImproveSSBond 2 

NameConform T0144.try12
OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 10 \
	pdb use_all scwrl_each
NameConform T0144.try12-opt
PrintConformPDB T0144.try12-opt.pdb edges

SCWRLconform
NameConform T0144.try12-opt-scwrl
PrintConformPDB T0144.try12-opt-scwrl.pdb 

CostConform
Time

quit