// To be run from pce/casp5/t0148

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0148.rand
Time


InFilePrefix 
ReadTemplateatoms Template.atoms

Include T0148.t2k.undertaker-align.script 
ReadFragmentAlignment T0148.t2k-2track-undertaker.a2m


infileprefix

Time

//ReadConformPDB robetta1.pdb
//    NameConform T0148.try7-robetta1
//ReadConformPDB robetta2.pdb
//    NameConform T0148.try7-robetta2
//ReadConformPDB robetta3.pdb
//    NameConform T0148.try7-robetta3
//ReadConformPDB robetta4.pdb
//    NameConform T0148.try7-robetta4
//ReadConformPDB robetta5.pdb
//    NameConform T0148.try7-robetta5

PopConform   // get rid of random conformation

//ReadConformPDB decoys/T0148.try8-opt-moved.pdb
//NameConform T0148.try11

//ReadConformPDB decoys/T0148.try12-try9.27.20.pdb
//NameConform T0148.try13-try12

//ReadConformPDB decoys/T0148.try7-opt-scwrl.pdb
//NameConform T0148.try12-try7

//ReadConformPDB decoys/T0148.try9-al10.pdb
//NameConform T0148.try12-try9-al

// ReadConformPDB decoys/T0148.try13-opt-scwrl.pdb
// NameConform T0148.try15-try13

//ReadConformPDB decoys/T0148.try12-try9.15.20.pdb
// NameConform T0148.try16-try12-15
//ReadConformPDB decoys/T0148.try7-robetta4.16.60.pdb
// NameConform T0148.try16-try7-17
//ReadConformPDB decoys/T0148.try13-al4.56.20.pdb
// NameConform T0148.try16-try13-56
//ReadConformPDB decoys/T0148.try13-al1.47.20.pdb
// NameConform T0148.try16-try13-47
//ReadConformPDB decoys/T0148.try13-try12.43.20.pdb
// NameConform T0148.try16-try13-43
//ReadConformPDB decoys/T0148.try15-opt.pdb
// NameConform T0148.try16-try15


// ReadConformPDB decoys/T0148.try12-try9-scwrl.70.20.pdb
//  NameConform T0148.try17-try9-70
// ReadConformPDB decoys/T0148.try7-robetta4.19.60.pdb
//  NameConform T0148.try17-try7-19
// ReadConformPDB decoys/T0148.try13-opt-scwrl.pdb
//  NameConform T0148.try17-try13
// ReadConformPDB decoys/T0148.try15-opt.pdb
//  NameConform T0148.try17-try15
// ReadConformPDB decoys/T0148.try16-opt.pdb
//  NameConform T0148.try17-try16

ReadConformPDB decoys/T0148.try15.14.20.pdb
    NameConform T0148.try19-try15-14
ReadConformPDB decoys/T0148.try16-opt.pdb
    NameConform T0148.try19-try16
ReadConformPDB decoys/T0148.try17.2.80.pdb
    NameConform T0148.try19-try17-2
ReadConformPDB decoys/T0148.try18.1.80.pdb
    NameConform T0148.try19-try18
ReadConformPDB decoys/T0148-moved17.pdb
    NameConform T0148.try19-moved
    
ReportCost undertaker-try19.rdb


//TryAllAlign shrink 0.4 min_keep_length 5 
//TryAllAlign shrink 0.4 min_keep_length 5 cumulative
//NameConform T0148.try14-al1
//PrintConformPDB T0148.try14-al1.pdb edges
 
//TryAllAlign shrink 0. min_keep_length 1 
//TryAllAlign shrink 0. min_keep_length 1 cumulative
//NameConform T0148.try14-al2
//PrintConformPDB T0148.try14-al2.pdb edges
 
//TryAllAlign shrink 0.3 min_keep_length 4 
//TryAllAlign shrink 0.3 min_keep_length 4 cumulative
//NameConform T0148.try14-al3
//PrintConformPDB T0148.try14-al3.pdb edges
 
//TryAllAlign shrink 0.1 min_keep_length 2 
//TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//NameConform T0148.try14-al4
//PrintConformPDB T0148.try14-al4.pdb edges
 
//TryAllAlign shrink 0.2 min_keep_length 3
//TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//NameConform T0148.try14-al5
//PrintConformPDB T0148.try14-al5.pdb edges
 
//TryAllAlign shrink 0. min_keep_length 1 
//TryAllAlign shrink 0. min_keep_length 1 cumulative
//NameConform T0148.try14-al6
//PrintConformPDB T0148.try14-al6.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	1efcA/
    include read-alignments.under 
infileprefix	1id0A/
    include read-alignments.under 
infileprefix	1dd3A/
    include read-alignments.under 
infileprefix	1ctf/
    include read-alignments.under 
infileprefix	1kvoA/
    include read-alignments.under 
infileprefix	1dlgA/
    include read-alignments.under 
infileprefix	1nawA/
    include read-alignments.under 
infileprefix	1etu/
    include read-alignments.under 
infileprefix	1d2eA/
    include read-alignments.under 
infileprefix	2oatA/
    include read-alignments.under 
infileprefix	1pytA/
    include read-alignments.under 
infileprefix	1hf2A/
    include read-alignments.under 
infileprefix	1fecA/
    include read-alignments.under 
infileprefix	1oatA/
    include read-alignments.under 
infileprefix	4aig/
    include read-alignments.under 
infileprefix	1faoA/
    include read-alignments.under 
infileprefix	1b8aA/
    include read-alignments.under 
infileprefix	1aye/
    include read-alignments.under 
infileprefix	1efm/
    include read-alignments.under 
infileprefix	1dg1G/
    include read-alignments.under 
infileprefix	1d8tA/
    include read-alignments.under 
infileprefix	1efuA/
    include read-alignments.under 


InFilePrefix 
ReadFragmentAlignment T0148.t2k.frag


OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 0.1 \
	ClashingRotamer 0.5 \
	OneRotamer 0.01 \
	InsertFragment 10 \
	CrossOver 0 \
	CrossAndInsert 4 \
	TwoFragment 3 \
	InsertSpecificFragment 4 \
	ReduceConstraint 3 \
	ReduceBreak 1 \
	CloseGap 0.1 \
	OptSubtree 0.05 \
	JiggleSubtree 0.05 \
	ReduceClash 1 \
	InsertSSBond 0

NameConform T0148.try19
OptConform pool_size 40 num_gen 80 gen_size 180 super_iter 10 \
	pdb  use_all
	// scwrl_each 
NameConform T0148.try19-opt
PrintConformPDB T0148.try19-opt.pdb edges

SCWRLconform
NameConform T0148.try19-opt-scwrl
PrintConformPDB T0148.try19-opt-scwrl.pdb
CostConform
Time

quit