// To be run from pce/casp5/t0171

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0171.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

ReadFragmentAlignment T0171-1a88A.vast-hand.a2m
ReadFragmentAlignment T0171-1broA.vast-hand.a2m

Time

// ReadConformPDB decoys/T0171.try1-opt-scwrl.pdb
// NameConform T0171.try2-try1

// ReadConformPDB decoys/T0171.try2-opt-scwrl.pdb
// NameConform T0171.try3-try2

// ReadConformPDB decoys/T0171.try3-opt.pdb
// NameConform T0171.try4-try3

// ReadConformPDB decoys/T0171.try3-opt.pdb
// NameConform T0171.try6-try3
// ReadConformPDB decoys/T0171.try4-opt.pdb
// NameConform T0171.try6-try4
// ReadConformPDB decoys/T0171.try5-opt.pdb
// NameConform T0171.try6-try5
// ReadConformPDB decoys/T0171.try4.0.100.pdb
// NameConform T0171.try6-try4-0
// ReadConformPDB decoys/T0171.try4.5.100.pdb
// NameConform T0171.try6-try4-5
// ReadConformPDB decoys/T0171.try4.8.100.pdb
// NameConform T0171.try6-try4-8

// ReadConformPDB decoys/T0171.try6.1.110.pdb
//   NameConform T0171.try7-try6-1
// ReadConformPDB decoys/T0171.try6-opt.pdb
//   NameConform T0171.try7-try6
// ReadConformPDB decoys/T0171.try6.5.110.pdb
//   NameConform T0171.try7-try6-5
// ReadConformPDB decoys/T0171.try6.4.110.pdb
//   NameConform T0171.try7-try6-4

// ReadConformPDB decoys/T0171.try7-try6-1.1.80.pdb
//     NameConform T0171.try8-try7-1
// ReadConformPDB decoys/T0171.try7.2.80.pdb
//     NameConform T0171.try8-try7-2
// ReadConformPDB decoys/T0171.try7-opt.pdb
//     NameConform T0171.try8-try7
// ReadConformPDB decoys/T0171.try7.0.80.pdb
//     NameConform T0171.try8-try7-0

// ReadConformPDB decoys/T0171-moved8.pdb
//    NameConform T0171.try9-moved
    
// ReadConformPDB decoys/T0171.try9-opt.pdb
//    NameConform T0171.try10-try9

ReadConformPDB decoys/T0171.try10.2.100.pdb
    NameConform T0171.try11-try10-2
ReadConformPDB decoys/T0171.try10.0.100.pdb
    NameConform T0171.try11-try10-0
ReadConformPDB decoys/T0171.try10.1.100.pdb
    NameConform T0171.try11-try10-1
ReadConformPDB decoys/T0171.try10.7.100.pdb
    NameConform T0171.try11-try10-7
ReadConformPDB decoys/T0171.try8-opt.pdb
    NameConform T0171.try11-try8
    
ReportCost undertaker-try11.rdb

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0171.try11-al2
// PrintConformPDB T0171.try11-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0171.try11-al4
// PrintConformPDB T0171.try11-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0171.try11-al6
// PrintConformPDB T0171.try11-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0171.try11-al8
//  PrintConformPDB T0171.try11-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0171.try11-al10
//  PrintConformPDB T0171.try11-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0171.try11-al12
//  PrintConformPDB T0171.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 T0171.t2k.frag

Include T0171.t2k.undertaker-align.script 
ReadFragmentAlignment T0171.t2k-2track-undertaker.a2m

InfilePrefix 1cr6B/
   include read-alignments.under
InfilePrefix 1ek1A/
   include read-alignments.under
InfilePrefix 1a8s/
   include read-alignments.under
InfilePrefix 1cqzA/
   include read-alignments.under
InfilePrefix 1a88A/
   include read-alignments.under
InfilePrefix 1bn7A/
   include read-alignments.under
InfilePrefix 1cqwA/
   include read-alignments.under
InfilePrefix 1ehyA/
   include read-alignments.under
InfilePrefix 1brt/
   include read-alignments.under
InfilePrefix 1a8q/
   include read-alignments.under
InfilePrefix 1bn6A/
   include read-alignments.under
InfilePrefix 1c4xA/
   include read-alignments.under
InfilePrefix

// 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 \
	ClashingRotamer 1 \
	OneRotamer 0.0 \
	InsertFragment 10 \
	CrossAndInsert 4 \
	TwoFragment 4 \
	InsertSpecificFragment 4 \
	ReduceBreak 1 \
	CloseGap 0.5 \
	ReduceClash 1 \
	JiggleSubtree 0.06 \
	OptSubtree 0.06 \
	InsertSSBond 0 \
	ImproveSSBond 1
	
NameConform T0171.try11
OptConform pool_size 70 num_gen 100 gen_size 160 super_iter 2 \
	scwrl_each pdb use_all
NameConform T0171.try11-opt
PrintConformPDB T0171.try11-opt.pdb edges
SCWRLConform
NameConform T0171.try11-opt-scwrl
PrintConformPDB T0171.try11-opt-scwrl.pdb

CostConform
Time

quit