// To be run from pce/casp5/t0155

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0155.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms
Include T0155.t2k.undertaker-align.script 
ReadFragmentAlignment T0155.t2k-2track-undertaker.a2m

InFilePrefix 1dhn/
Include read-alignments.under
InFilePrefix 1b9lA/
Include read-alignments.under

InFilePrefix 

Time

// ReadConformPDB decoys/T0155.try3-opt-scwrl.pdb
// ReadConformPDB decoys/T0155.try4-opt.pdb
// ReadConformPDB decoys/T0155.try4.12.20.pdb

// ReadConformPDB decoys/T0155.try5-opt-scwrl.pdb
// NameConform T0155.try6-try5
// ReadConformPDB decoys/T0155.try5-al2.12.20.pdb
// NameConform T0155.try6-try5-12

// ReadConformPDB decoys/T0155.try6-try5.12.80.pdb
//  NameConform T0155.try7-try6-12
// ReadConformPDB decoys/T0155.try6-try5.10.80.pdb
//  NameConform T0155.try7-try6-10
// ReadConformPDB decoys/T0155.try6.15.80.pdb
//  NameConform T0155.try7-try6-15
// ReadConformPDB decoys/T0155.try6-try5.14.80.pdb
//  NameConform T0155.try7-try6-14
// ReadConformPDB decoys/T0155.try6.9.80.pdb
//  NameConform T0155.try7-try6-9


// ReadConformPDB decoys/T0155.try7-opt.pdb
// NameConform T0155.try8-try7

// ReadConformPDB decoys/T0155.try8-opt.pdb
// NameConform T0155.try9-try8

// ReadConformPDB decoys/T0155.try9.16.100.pdb
//  NameConform T0155.try10-try9-16
// ReadConformPDB decoys/T0155.try9.12.100.pdb
//  NameConform T0155.try10-try9-12
// ReadConformPDB decoys/T0155.try9.6.100.pdb
//  NameConform T0155.try10-try9-6
// ReadConformPDB decoys/T0155.try9.10.100.pdb
//  NameConform T0155.try10-try9-10
// ReadConformPDB decoys/T0155.try9.11.100.pdb
//  NameConform T0155.try10-try9-11
// ReadConformPDB decoys/T0155.try9.19.100.pdb
//  NameConform T0155.try10-try9-19
// ReadConformPDB decoys/T0155.try9.20.100.pdb
//  NameConform T0155.try10-try9-20
// ReadConformPDB decoys/T0155.try9-opt.pdb
//  NameConform T0155.try10-try9

// ReadConformPDB decoys/T0155.try9-opt.pdb
//   NameConform T0155.try11-try9
// ReadConformPDB decoys/T0155.try10-opt.pdb
//   NameConform T0155.try11-try10
// ReadConformPDB decoys/T0155.try10-try9-10.7.80.pdb
//   NameConform T0155.try11-try10-7
// ReadConformPDB decoys/T0155.try10-try9-10.16.80.pdb
//   NameConform T0155.try11-try10-16
// ReadConformPDB decoys/T0155.try10-try9-12.11.80.pdb
//   NameConform T0155.try11-try10-11
// ReadConformPDB decoys/T0155.try10-try9-12.9.80.pdb
//   NameConform T0155.try11-try10-9


// ReadConformPDB decoys/T0155.try11.7.90.pdb
//    NameConform T0155.try11-try11-7
// ReadConformPDB decoys/T0155.try11.12.90.pdb
//    NameConform T0155.try11-try11-12
// ReadConformPDB decoys/T0155.try11.6.90.pdb
//    NameConform T0155.try11-try11-6
// ReadConformPDB decoys/T0155.try11.0.90.pdb
//    NameConform T0155.try11-try11-0
// ReadConformPDB decoys/T0155.try11.23.90.pdb
//    NameConform T0155.try11-try11-23
// ReadConformPDB decoys/T0155.try11.19.90.pdb
//    NameConform T0155.try11-try11-19
// ReadConformPDB decoys/T0155.try11.11.90.pdb
//    NameConform T0155.try11-try11-11

ReadConformPDB decoys/T0155.try12.4.90.pdb
    NameConform T0155.try13-try12-4
ReadConformPDB decoys/T0155.try12.10.90.pdb
    NameConform T0155.try13-try12-10
ReadConformPDB decoys/T0155.try12.22.90.pdb
    NameConform T0155.try13-try12-22
ReadConformPDB decoys/T0155.try12.5.90.pdb
    NameConform T0155.try13-try12-5
ReadConformPDB decoys/T0155.try12.13.90.pdb
    NameConform T0155.try13-try12-13
ReadConformPDB decoys/T0155.try12.14.90.pdb
    NameConform T0155.try13-try12-14


ReportCost undertaker-try13.rdb

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0155.try13-al2
// PrintConformPDB T0155.try13-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0155.try13-al4
// PrintConformPDB T0155.try13-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0155.try13-al6
// PrintConformPDB T0155.try13-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0155.try13-al8
//  PrintConformPDB T0155.try13-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0155.try13-al10
//  PrintConformPDB T0155.try13-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0155.try13-al12
//  PrintConformPDB T0155.try13-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 T0155.t2k.frag

OutFilePrefix
Printtemplateatoms Template.atoms
OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 0.3 \
	ClashingRotamer 0.5 \
	InsertFragment 3 \
	CrossAndInsert 9 \
	Crossover 0 \
	TwoFragment 3 \
	InsertSpecificFragment 5 \
	ReduceBreak 1 \
	CloseGap 0.3 \
	jiggleSubtree 0.04 \
	OptSubtree 0.04 \
	ReduceClash 1 \
	InsertSSBond 0

NameConform T0155.try13
OptConform pool_size 70 num_gen 60 gen_size 200 super_iter 20 \
	pdb use_all scwrl_each
NameConform T0155.try13-opt
PrintConformPDB T0155.try13-opt.pdb edges
SCWRLConform
NameConform T0155.try13-opt-scwrl
PrintConformPDB T0155.try13-opt-scwrl.pdb 

CostConform
Time

quit