// To be run from pce/casp5/t0150

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/


InfilePrefix 
ReadTemplateAtoms Template.atoms

InFilePrefix 1ck9A/
Include read-alignments.under
InFilePrefix 1jj2F/
Include read-alignments.under
InFilePrefix 1ffkE/
Include read-alignments.under
InFilePrefix 1e7kA/
Include read-alignments.under
InFilePrefix 1dt9A/
Include read-alignments.under

InFilePrefix 

Include T0150.t2k.undertaker-align.script 
ReadFragmentAlignment T0150.t2k-2track-undertaker.a2m

Time

// ReadConformPDB decoys/T0150.try4-opt-scwrl.pdb
//  NameConform T0150.try5-try4

// ReadConformPDB decoys/T0150.try5-opt.pdb
//   NameConform T0150.try6-try6

// ReadConformPDB decoys/T0150.try7-opt.pdb
//    NameConform T0150.try8-try7
    

ReadConformPDB decoys/T0150.try7-opt.pdb
    NameConform T0150.try9-try7
ReadConformPDB decoys/T0150.try5-opt.pdb
    NameConform T0150.try9-try5
ReadConformPDB decoys/T0150.try6-opt.pdb
    NameConform T0150.try9-try6
ReadConformPDB decoys/T0150.try8-opt-scwrl.pdb
    NameConform T0150.try9-try8
ReadConformPDB decoys/T0150.try6.2.100.pdb
    NameConform T0150.try9-try6-2
    

ReportCost undertaker-try9.rdb

// ConformFromSeq replace // get a random conformation, removing all-zero one
// NameConform T0150.rand
// Time
   
//    TryAllAlign shrink 0.4 min_keep_length 5 
//    TryAllAlign shrink 0.4 min_keep_length 5 cumulative
//   NameConform T0150.try9-al2
//   PrintConformPDB T0150.try9-al2.pdb edges
 
//   TryAllAlign shrink 0. min_keep_length 1 
//   TryAllAlign shrink 0. min_keep_length 1 cumulative
//   NameConform T0150.try9-al4
//   PrintConformPDB T0150.try9-al4.pdb edges
 
//    TryAllAlign shrink 0.3 min_keep_length 4 
//    TryAllAlign shrink 0.3 min_keep_length 4 cumulative
//   NameConform T0150.try9-al6
//   PrintConformPDB T0150.try9-al6.pdb edges
 
//   TryAllAlign shrink 0.1 min_keep_length 2 
//   TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//    NameConform T0150.try9-al8
//    PrintConformPDB T0150.try9-al8.pdb edges
 
//   TryAllAlign shrink 0.2 min_keep_length 3
//   TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//    NameConform T0150.try9-al10
//    PrintConformPDB T0150.try9-al10.pdb edges
 
//    TryAllAlign shrink 0. min_keep_length 1 
//    TryAllAlign shrink 0. min_keep_length 1 cumulative
//    NameConform T0150.try9-al12
//    PrintConformPDB T0150.try9-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 T0150.t2k.frag
InFilePrefix 



OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time



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

NameConform T0150.try9
OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 30 \
	pdb scwrl_each use_all
NameConform T0150.try9-opt
PrintConformPDB T0150.try9-opt.pdb edges

SCWRLconform
NameConform T0150.try9-opt-scwrl
PrintConformPDB T0150.try9-opt-scwrl.pdb
CostConform
Time

quit