// To be run from pce/casp5/t0151

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0151.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0151.t2k.undertaker-align.script 
ReadFragmentAlignment T0151.t2k-2track-undertaker.a2m

InFilePrefix 1qvcA/
Include read-alignments.under
InFilePrefix 1kawA/
Include read-alignments.under
InFilePrefix 3ullA/
Include read-alignments.under
InFilePrefix 1eygA/
Include read-alignments.under
InFilePrefix 1otcA/
Include read-alignments.under
InFilePrefix 1quqA/
Include read-alignments.under

InFilePrefix
Time

// ReadConformPDB decoys/T0151.try1-opt.pdb
/// NameConform T0151.try2-try1

// ReadConformPDB decoys/T0151.try1-opt.pdb
// NameConform T0151.try3-try1

// ReadConformPDB decoys/T0151.try2-opt.pdb
// NameConform T0151.try3-try2

// ReadConformPDB decoys/T0151.try1-opt.pdb
// NameConform T0151.try4-try1

// ReadConformPDB decoys/T0151.try2-opt.pdb
// NameConform T0151.try4-try2

// ReadConformPDB decoys/T0151.try3-opt.pdb
// NameConform T0151.try4-try3

// ReadConformPDB decoys/T0151.try3.17.50.pdb
// NameConform T0151.try4-try3-17

// ReadConformPDB decoys/T0151.try3.11.50.pdb
// NameConform T0151.try4-try3-11

// ReadConformPDB decoys/T0151.try4.18.40.pdb
// NameConform T0151.try5-try4-18
// ReadConformPDB decoys/T0151.try4.10.40.pdb
// NameConform T0151.try5-try4-10
// ReadConformPDB decoys/T0151.try4.15.40.pdb
// NameConform T0151.try5-try4-15
// ReadConformPDB decoys/T0151.try4.7.40.pdb
// NameConform T0151.try5-try4-7

// ReadConformPDB decoys/T0151.try4.6.40.pdb
// NameConform T0151.try5-try4-6

ReadConformPDB decoys/T0151.try5-opt.pdb
NameConform T0151.try6-try5
ReadConformPDB decoys/T0151.try5.20.50.pdb
NameConform T0151.try6-try5-20
ReadConformPDB decoys/T0151.try5.7.50.pdb
NameConform T0151.try6-try5-7
ReadConformPDB decoys/T0151.try5.1.50.pdb
NameConform T0151.try6-try5-1
ReadConformPDB decoys/T0151.try5.17.50.pdb
NameConform T0151.try6-try5-17
ScwrlConform
NameConform T0151.try6-try5-17-s

ReportCost undertaker-try6.rdb


// TryAllAlign shrink 0.4 min_keep_length 5 
// TryAllAlign shrink 0.4 min_keep_length 5 cumulative
//NameConform T0151.try1-al2
//PrintConformPDB T0151.try1-al2.pdb edges
 
//TryAllAlign shrink 0. min_keep_length 1 
//TryAllAlign shrink 0. min_keep_length 1 cumulative
//NameConform T0151.try1-al4
//PrintConformPDB T0151.try1-al4.pdb edges
 
// TryAllAlign shrink 0.3 min_keep_length 4 
// TryAllAlign shrink 0.3 min_keep_length 4 cumulative
//NameConform T0151.try1-al6
//PrintConformPDB T0151.try1-al6.pdb edges
 
//TryAllAlign shrink 0.1 min_keep_length 2 
//TryAllAlign shrink 0.1 min_keep_length 2 cumulative
// NameConform T0151.try1-al8
// PrintConformPDB T0151.try1-al8.pdb edges
 
//TryAllAlign shrink 0.2 min_keep_length 3
//TryAllAlign shrink 0.2 min_keep_length 3 cumulative
// NameConform T0151.try1-al10
// PrintConformPDB T0151.try1-al10.pdb edges
 
// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0151.try1-al12
// PrintConformPDB T0151.try1-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 T0151.t2k.frag


OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 0.1 \
	ClashingRotamer 0.5 \
	InsertFragment 1 \
	Crossover 0.1 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 0.5 \
	ReduceBreak 9 \
	CloseGap 0.4 \
	OptSubtree 0.04 \
	JiggleSubtree 0.04 \
	ReduceClash 1 \
	InsertSSBond 0

NameConform T0151.try6
OptConform pool_size 60 num_gen 50 gen_size 170 super_iter 20 \
	pdb use_all scwrl_each
NameConform T0151.try6-opt
PrintConformPDB T0151.try6-opt.pdb edges

SCWRLConform
NameConform T0151.try6-opt-scwrl
PrintConformPDB T0151.try6-opt-scwrl.pdb 


CostConform
Time

quit