// To be run from pce/casp5/t0162

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0162.t2k.undertaker-align.script 
ReadFragmentAlignment T0162.t2k-2track-undertaker.a2m

InFilePrefix

Time

// ReadConformPDB robetta5.pdb
//     NameConform T0162.try3-robetta5
// ReadConformPDB robetta4.pdb
//     NameConform T0162.try3-robetta4
// ReadConformPDB robetta3.pdb
//     NameConform T0162.try3-robetta3
// ReadConformPDB robetta2.pdb
//     NameConform T0162.try3-robetta2
// ReadConformPDB robetta1.pdb
//     NameConform T0162.try3-robetta1

//ReadConformPDB decoys/T0162.try2-opt-scwrl.pdb
//	NameConform T0162.try4-try2
//ReadConformPDB decoys/T0162.try3-robetta5.10.20.pdb
//	NameConform T0162.try4-try3-10
//ReadConformPDB decoys/T0162.try3-robetta3.0.20.pdb
//	NameConform T0162.try4-try3-0


// ReadConformPDB decoys/T0162.try4-try3-10-scwrl.10.80.pdb
// 	NameConform T0162.try5-try4

//ReadConformPDB decoys/T0162.try4-opt.pdb
//	NameConform T0162.try6-try4
//ReadConformPDB decoys/T0162.try5.0.80.pdb
//	NameConform T0162.try6-try5-0
//ReadConformPDB decoys/T0162.try5.1.80.pdb
//	NameConform T0162.try6-try5-1
//ReadConformPDB decoys/T0162.try5.2.80.pdb
//	NameConform T0162.try6-try5-2
//ReadConformPDB decoys/T0162.try5.3.80.pdb
//	NameConform T0162.try6-try5-3
//ReadConformPDB decoys/T0162.try5.4.80.pdb
//	NameConform T0162.try6-try5-4


// ReadConformPDB decoys/T0162.try6-opt.pdb
// NameConform T0162.try8-try6-1
// ReadConformPDB decoys/T0162.try6-try5-3.0.100.pdb
// NameConform T0162.try8-try6-2

// ReadConformPDB decoys/T0162.try1.1.20.pdb
//  NameConform T0162.try9-try1-1
// ReadConformPDB decoys/T0162.try2.17.20.pdb
//  NameConform T0162.try9-try2-17
// ReadConformPDB decoys/T0162.try3-robetta5+T0162-3gbp-simpleSW-adpstyle5.pw.a2m.gz:3gbp.3.20.pdb	
//  NameConform T0162.try9-try3-3
// ReadConformPDB decoys/T0162.try4-try3-10.2.80.pdb
//  NameConform T0162.try9-try4-2
// ReadConformPDB decoys/T0162.try5.3.80.pdb
//  NameConform T0162.try9-try5-3
// ReadConformPDB decoys/T0162.try6-opt.pdb
//  NameConform T0162.try9-try6
// ReadConformPDB decoys/T0162.try7-opt-scwrl.pdb
//  NameConform T0162.try9-try7
// ReadConformPDB decoys/T0162.try8-try6-1+T0162-3gbp-v...+T0162-1dzgI-vit-adpstyle1.pw.a2m.gz:1dzgI.4.100.pdb
//  NameConform T0162.try9-try8-4
// ReadConformPDB decoys/T0162.try8+T0162-1a2vA-2track-protein-STR-local-adpstyle1.pw.a2m.gz:1a2vA.0.100.pdb
//  NameConform T0162.try9-try8-0

// ReadConformPDB decoys/T0162.try1.1.20.pdb
//  NameConform T0162.try10-try1-1
// ReadConformPDB decoys/T0162.try2.17.20.pdb
//  NameConform T0162.try10-try2-17
// ReadConformPDB decoys/T0162.try3-robetta5+T0162-3gbp-simpleSW-adpstyle5.pw.a2m.gz:3gbp.3.20.pdb	
//  NameConform T0162.try10-try3-3
// ReadConformPDB decoys/T0162.try4-try3-10.2.80.pdb
//  NameConform T0162.try10-try4-2
// ReadConformPDB decoys/T0162.try5.3.80.pdb
//  NameConform T0162.try10-try5-3
// ReadConformPDB decoys/T0162.try7-opt-scwrl.pdb
//  NameConform T0162.try10-try7
// ReadConformPDB decoys/T0162.try8-try6-1+T0162-3gbp-v...+T0162-1dzgI-vit-adpstyle1.pw.a2m.gz:1dzgI.4.100.pdb
//  NameConform T0162.try10-try8-4
// ReadConformPDB decoys/T0162.try8+T0162-1a2vA-2track-protein-STR-local-adpstyle1.pw.a2m.gz:1a2vA.0.100.pdb
//  NameConform T0162.try10-try8-0


// ReadConformPDB decoys/T0162.try7-opt-scwrl.pdb
//   NameConform T0162.try11-try7
// ReadConformPDB decoys/T0162.try8+T0162-1a2vA-2track-protein-STR-local-adpstyle1.pw.a2m.gz:1a2vA.0.100.pdb	
//     NameConform T0162.try11-try8-0
// ReadConformPDB decoys/T0162.try9-opt-scwrl.pdb
//     NameConform T0162.try11-try9
// ReadConformPDB decoys/T0162.try10-try8-4.0.100.pdb
//     NameConform T0162.try11-try10-0

// ReadConformPDB decoys/T0162.try8-opt.pdb
//      NameConform T0162.try12-try8
// ReadConformPDB decoys/T0162.try9-opt-scwrl.pdb
//      NameConform T0162.try12-try9
// ReadConformPDB decoys/T0162.try10-opt.pdb
//      NameConform T0162.try12-try10
// ReadConformPDB decoys/T0162.try11-opt.pdb
//      NameConform T0162.try12-try11



// ReadConformPDB decoys/T0162.try6-opt.pdb
//       NameConform T0162.try13-try6
// ReadConformPDB decoys/T0162.try7-opt-scwrl.pdb
//       NameConform T0162.try13-try7
// ReadConformPDB decoys/T0162.try8-opt.pdb
//       NameConform T0162.try13-try8
// ReadConformPDB decoys/T0162.try9-opt.pdb
//       NameConform T0162.try13-try9
// ReadConformPDB decoys/T0162.try10-opt.pdb
//       NameConform T0162.try13-try10
// ReadConformPDB decoys/T0162.try11-opt.pdb
//       NameConform T0162.try13-try11
// ReadConformPDB decoys/T0162.try12-opt.pdb
//       NameConform T0162.try13-try12



//ReadConformPDB decoys/T0162.try6-opt.pdb
//      NameConform T0162.try14-try6
//ReadConformPDB decoys/T0162.try7-opt-scwrl.pdb
//     NameConform T0162.try14-try7
//ReadConformPDB decoys/T0162.try8-opt.pdb
//      NameConform T0162.try14-try8
//ReadConformPDB decoys/T0162.try9-opt.pdb
//      NameConform T0162.try14-try9
//ReadConformPDB decoys/T0162.try10-opt.pdb
//      NameConform T0162.try14-try10
//ReadConformPDB decoys/T0162.try11-opt-scwrl.pdb
//      NameConform T0162.try14-try11
//ReadConformPDB decoys/T0162.try12-opt.pdb
//      NameConform T0162.try14-try12
      

//ReadConformPDB decoys/T0162.try6-opt.pdb
//NameConform T0162.try19-try6
//ReadConformPDB decoys/T0162.try10-opt.pdb
//NameConform T0162.try19-try10
//ReadConformPDB decoys/T0162.try7-opt-scwrl.pdb
//NameConform T0162.try19-try7
ReadConformPDB decoys/T0162.try17-try6.0.120-moved.pdb
NameConform T0162.try20-try17-moved

ReportCost undertaker-try20.rdb

// ConformFromSeq	replace // get a random conformation, removing all-zero one
// NameConform T0162.rand
// Time

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0162.try4-al2
// PrintConformPDB T0162.try4-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0162.try4-al4
// PrintConformPDB T0162.try4-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0162.try4-al6
// PrintConformPDB T0162.try4-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0162.try4-al8
//  PrintConformPDB T0162.try4-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0162.try4-al10
//  PrintConformPDB T0162.try4-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0162.try4-al12
//  PrintConformPDB T0162.try4-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	1b3jA/
    include read-alignments.under 
InfilePrefix	3gbp/
    include read-alignments.under 
InfilePrefix	8rucI/
    include read-alignments.under 
InfilePrefix	1rboC/
    include read-alignments.under 
InfilePrefix	1hyrC/
    include read-alignments.under 
InfilePrefix	1a2vA/
    include read-alignments.under 
InfilePrefix	1gcyA/
    include read-alignments.under 
InfilePrefix	1yasA/
    include read-alignments.under 
InfilePrefix	1dzgI/
    include read-alignments.under 
InfilePrefix	1zagB/
    include read-alignments.under 
InfilePrefix	1qj4A/
    include read-alignments.under 

InFilePrefix 
ReadFragmentAlignment T0162.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 2 \
	ClashingRotamer 0.5 \
	OneRotamer 0.01 \
	InsertFragment 9 \
	CrossAndInsert 2 \
	CrossOver 0 \
	TwoFragment 1 \
	InsertSpecificFragment 5 \
	ReduceBreak 1 \
	CloseGap 0.3 \
	ReduceClash 1 \
	JiggleSubtree 0.03 \
	OptSubtree 0.07 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0162.try20
OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 1 \
	pdb use_all 
	// scwrl_each
NameConform T0162.try20-opt
PrintConformPDB T0162.try20-opt.pdb edges
SCWRLConform
NameConform T0162.try20-opt-scwrl
PrintConformPDB T0162.try20-opt-scwrl.pdb

CostConform
Time

quit


//  The following parameter setting was used for try3 to
//	pull the robetta models together.
// InitMethodProbs InsertAlignment 0.3 \
// 	ClashingRotamer 0.5 \
// 	InsertFragment 8 \
// 	CrossAndInsert 1 \
// 	CrossOver 0 \
// 	TwoFragment 1 \
// 	InsertSpecificFragment 5 \
// 	ReduceBreak 5 \
// 	CloseGap 0.1 \
// 	ReduceClash 1 \
// 	JiggleSubtree 0.03 \
// 	OptSubtree 3 \
// 	InsertSSBond 0 \
// 	ImproveSSBond 0
// 	
// // NameConform T0162.try4
// OptConform pool_size 40 num_gen 20 gen_size 120 super_iter 20 \
// 	pdb use_all scwrl_each no_initial_fill