// To be run from pce/casp5/t0189

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0189.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0189.t2k.undertaker-align.script 
ReadFragmentAlignment T0189.t2k-2track-undertaker.a2m

InfilePrefix	1rkd/
	include read-alignments.under 
InfilePrefix	1bx4A/
	include read-alignments.under 
InfilePrefix	1liiA/
	include read-alignments.under 
InfilePrefix	1lioA/
	include read-alignments.under 
InfilePrefix	1dgmA/
	include read-alignments.under 
InfilePrefix	1jxhA/
	include read-alignments.under 
InfilePrefix	1c3qA/
	include read-alignments.under 
InfilePrefix	1gc5A/
	include read-alignments.under 
InfilePrefix	1ekqA/
	include read-alignments.under 


InfilePrefix

Time

// ReadConformPdb decoys/T0189.try1-opt-scwrl.pdb
//    NameConform T0189.try2-try1

// ReadConformPdb decoys/T0189.try1-opt-scwrl.pdb
//     NameConform T0189.try4-try1
// ReadConformPdb decoys/T0189.try2-opt.pdb
//     NameConform T0189.try4-try2
// ReadConformPdb decoys/T0189.try3-opt.pdb
//     NameConform T0189.try4-try3


// ReadConformPdb decoys/T0189.try2-opt.pdb
//     NameConform T0189.try5-try2
// ReadConformPdb decoys/T0189.try3-opt.pdb
//     NameConform T0189.try5-try3
// ReadConformPdb decoys/T0189.try3.1.100.pdb
//     NameConform T0189.try5-try3-1
// ReadConformPdb decoys/T0189.try3.2.100.pdb
//     NameConform T0189.try5-try3-2
// ReadConformPdb decoys/T0189.try4.1.100.pdb
//     NameConform T0189.try5-try4-1
// ReadConformPdb decoys/T0189.try4.0.100.pdb
//     NameConform T0189.try5-try4-0
    
// ReadConformPdb decoys/T0189.try2-opt.pdb
//     NameConform T0189.try6-try2
// ReadConformPdb decoys/T0189.try3-opt.pdb
//     NameConform T0189.try6-try3
// ReadConformPdb decoys/T0189.try4.1.100.pdb
//     NameConform T0189.try6-try4-1
// ReadConformPdb decoys/T0189.try4.0.100.pdb
//     NameConform T0189.try6-try4-0	
// ReadConformPdb decoys/T0189.try5-opt.pdb
//     NameConform T0189.try6-try5

ReadConformPdb decoys/T0189.try3-opt.pdb
    NameConform T0189.try7-try3
ReadConformPdb decoys/T0189.try4.1.100.pdb
    NameConform T0189.try7-try4-1
ReadConformPdb decoys/T0189.try4.0.100.pdb
    NameConform T0189.try7-try4-0	
ReadConformPdb decoys/T0189.try5-opt.pdb
    NameConform T0189.try7-try5
ReadConformPdb decoys/T0189.try6-opt.pdb
    NameConform T0189.try7-try6

ReportCost undertaker-try7.rdb

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0189.try7-al2
// PrintConformPDB T0189.try7-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0189.try7-al4
// PrintConformPDB T0189.try7-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0189.try7-al6
// PrintConformPDB T0189.try7-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0189.try7-al8
//  PrintConformPDB T0189.try7-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0189.try7-al10
//  PrintConformPDB T0189.try7-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0189.try7-al12
//  PrintConformPDB T0189.try7-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 T0189.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 \
	OneRotamer 0.01 \
	ClashingRotamer 1 \
	InsertFragment 10 \
	CrossAndInsert 5 \
	TwoFragment 20 \
	InsertSpecificFragment 5 \
	ReduceBreak 10 \
	CloseGap 0.3 \
	ReduceClash 2 \
	ReduceConstraint 5 \
	JiggleSubtree 0.01 \
	OptSubtree 0.01 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0189.try7
OptConform pool_size 40 num_gen 200 gen_size 140 super_iter 1 \
	pdb use_all
	// scwrl_each
NameConform T0189.try7-opt
PrintConformPDB T0189.try7-opt.pdb edges
SCWRLConform
NameConform T0189.try7-opt-scwrl
PrintConformPDB T0189.try7-opt-scwrl.pdb

CostConform
Time

quit