// 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 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.try9-try5
// ReadConformPDB decoys/T0194.try6.0.60.pdb
// NameConform T0186.try9-try6-0
// ReadConformPDB decoys/T0194.try6.1.60.pdb
// NameConform T0186.try9-try6-1

ReadConformPDB decoys/T0194.try2-opt-scwrl.pdb
 NameConform T0186.try11-try2
ReadConformPDB decoys/T0194.try4.17.60.pdb
 NameConform T0186.try11-try4-17
ReadConformPDB decoys/T0194.try2.4.60.pdb
 NameConform T0186.try11-try2-4
ReadConformPDB decoys/T0194.try4.0.60.pdb
 NameConform T0186.try11-try4-0
ReadConformPDB decoys/T0194.try3.18.60.pdb
 NameConform T0186.try11-try3-18
ReadConformPDB decoys/T0194.try9-opt.pdb
 NameConform T0186.try11-try9

Time

ReportCost undertaker-try11.rdb

// TryAllAlign shrink 0.4 min_keep_length 5 
// TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0194.try11-al2
// PrintConformPDB T0194.try11-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0194.try11-al4
// PrintConformPDB T0194.try11-al4.pdb edges

// TryAllAlign shrink 0.3 min_keep_length 4 
// TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0194.try11-al6
// PrintConformPDB T0194.try11-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
// NameConform T0194.try11-al8
// PrintConformPDB T0194.try11-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
// NameConform T0194.try11-al10
// PrintConformPDB T0194.try11-al10.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0194.try11-al12
// PrintConformPDB T0194.try11-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.try11
OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 1 \
	use_all pdb
NameConform T0194.try11-opt
PrintConformPDB T0194.try11-opt.pdb edges
// SCWRLConform
// NameConform T0194.try11-opt-scwrl
// PrintConformPDB T0194.try11-opt-scwrl.pdb

CostConform
Time

quit