// To be run from pce/casp5/t0194

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0194.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0194.t2k.undertaker-align.script 
ReadFragmentAlignment T0194.t2k-2track-undertaker.a2m

InFilePrefix 1d2nA/
    include read-alignments.under 


//InFilePrefix 1bdg/
//    include read-alignments.under 
//InFilePrefix 1opy/
//    include read-alignments.under 
//InFilePrefix 1heuA/
//    include read-alignments.under 
//InFilePrefix 1ee2A/
//    include read-alignments.under 
//InFilePrefix 1hetA/
//    include read-alignments.under 
//InFilePrefix 1qi6A/
//    include read-alignments.under 
//InFilePrefix 1euhA/
//    include read-alignments.under 
//InFilePrefix 1xze/
//    include read-alignments.under 
//InFilePrefix 1d2nA/
//   include read-alignments.under 
//InFilePrefix 9gacA/
//    include read-alignments.under 
//InFilePrefix 2pgd/
//    include read-alignments.under 
//InFilePrefix 1e32A/
//    include read-alignments.under 
//InFilePrefix 1g6oA/
//    include read-alignments.under 
//InFilePrefix 1jbkA/
//    include read-alignments.under 
//InFilePrefix 1d2mA/
//    include read-alignments.under 

InfilePrefix


// ReadConformPDB decoys/T0194.try2-opt-scwrl.pdb
// NameConform T0186.try6-try2
// ReadConformPDB decoys/T0194.try3-opt-scwrl.pdb
// NameConform T0186.try6-try3
// ReadConformPDB decoys/T0194.try5-opt-scwrl.pdb
// NameConform T0186.try6-try3

// ReadConformPDB decoys/T0194.try5-opt-scwrl.pdb
//  NameConform T0186.try8-try5
// ReadConformPDB decoys/T0194.try6.0.60.pdb
//  NameConform T0186.try8-try6-0
// ReadConformPDB decoys/T0194.try6.1.60.pdb
//  NameConform T0186.try8-try6-1

//ReadConformPDB decoys/T0194.try5-opt-scwrl.pdb
// NameConform T0186.try12-try5
//ReadConformPDB decoys/T0194.try6.0.60.pdb
// NameConform T0186.try12-try6-0
//ReadConformPDB decoys/T0194.try6.1.60.pdb
// NameConform T0186.try12-try6-1


Time

ReportCost undertaker-try12.rdb

 TryAllAlign shrink 0.4 min_keep_length 5 
 TryAllAlign shrink 0.4 min_keep_length 5 cumulative
 NameConform T0194.try12-al2
 PrintConformPDB T0194.try12-al2.pdb edges

 TryAllAlign shrink 0. min_keep_length 1 
 TryAllAlign shrink 0. min_keep_length 1 cumulative
 NameConform T0194.try12-al4
 PrintConformPDB T0194.try12-al4.pdb edges

 TryAllAlign shrink 0.3 min_keep_length 4 
 TryAllAlign shrink 0.3 min_keep_length 4 cumulative
 NameConform T0194.try12-al6
 PrintConformPDB T0194.try12-al6.pdb edges

 TryAllAlign shrink 0.1 min_keep_length 2 
 TryAllAlign shrink 0.1 min_keep_length 2 cumulative
 NameConform T0194.try12-al8
 PrintConformPDB T0194.try12-al8.pdb edges

 TryAllAlign shrink 0.2 min_keep_length 3
 TryAllAlign shrink 0.2 min_keep_length 3 cumulative
 NameConform T0194.try12-al10
 PrintConformPDB T0194.try12-al10.pdb edges

 TryAllAlign shrink 0. min_keep_length 1 
 TryAllAlign shrink 0. min_keep_length 1 cumulative
 NameConform T0194.try12-al12
 PrintConformPDB T0194.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.

InFilePrefix 
ReadFragmentAlignment T0194.t2k.frag

// The next 3 lines save the templates in a single file, to avoid having
// to reread the PDB files.  Note that ReadTemplateAtoms should be called
// before any ReadFragmentAlignments to take full advantage of this
// cached results.
OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time


InitMethodProbs InsertAlignment 0.3 \
	ClashingRotamer 0.5 \
	OneRotamer 0.02 \
	InsertFragment 10 \
	CrossAndInsert 10 \
	CrossOver 0 \
	TwoFragment 10 \
	InsertSpecificFragment 10 \
	ReduceBreak 5 \
	CloseGap 0.1 \
	ReduceClash 1 \
	ReduceConstraint 1 \
	JiggleSubtree 0.03 \
	OptSubtree 0.03 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0194.try12
OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 5 \
	use_all pdb
NameConform T0194.try12-opt
PrintConformPDB T0194.try12-opt.pdb edges
// SCWRLConform
// NameConform T0194.try12-opt-scwrl
// PrintConformPDB T0194.try12-opt-scwrl.pdb

CostConform
Time

quit