// To be run from pce/casp5/t0140

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time



OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0140.rand
Time



// The following alignments are believed to be good:

InFilePrefix 
ReadTemplateAtoms Template.atoms

ReadFragmentAlignment T0140.t2k-2track-undertaker.a2m
Include T0140.undertaker-align.script 

InfilePrefix 1mjc/
  include read-alignments.under
InfilePrefix 3mefA/
  include read-alignments.under
InfilePrefix 1sro/
  include read-alignments.under
InfilePrefix 1go3E/
  include read-alignments.under
InfilePrefix 1c9oA/
  include read-alignments.under
InfilePrefix 1kl9A/
  include read-alignments.under
InfilePrefix 1e3pA/
  include read-alignments.under
InfilePrefix 1h95A/
  include read-alignments.under
InfilePrefix 1g6pA/
  include read-alignments.under

InfilePrefix

Time

// ReadConformPDB decoys/T0140.try6-opt-scwrl.pdb
// NameConform T0140.try7-try6

// ReadConformPDB decoys/T0140.try6-al6.8.80.pdb
// NameConform T0140.try7-try6-8

// ReadConformPDB decoys/T0140.try6-opt-scwrl.pdb
// NameConform T0140.try8-try6
// ReadConformPDB decoys/T0140.try7-opt-scwrl.pdb
// NameConform T0140.try8-try7

// ReadConformPDB decoys/T0140.try6-opt-scwrl.pdb
// NameConform T0140.try9-try6
// ReadConformPDB decoys/T0140.try7-opt-scwrl.pdb
// NameConform T0140.try9-try7
// ReadConformPDB decoys/T0140.try8-opt.pdb
// NameConform T0140.try9-try8
// ReadConformPDB decoys/T0140.try8.15.90.pdb
// NameConform T0140.try9-try8-15
// ReadConformPDB decoys/T0140.try8.2.90.pdb
// NameConform T0140.try9-try8-2
// ReadConformPDB decoys/T0140.try8.29.90.pdb
// NameConform T0140.try9-try8-29
// ReadConformPDB decoys/T0140.try8.11.90.pdb
// NameConform T0140.try9-try8-11

// ReadConformPDB decoys/T0140.try9-opt.pdb
// NameConform T0140.try10-try9

// ReadConformPDB decoys/T0140.try9-opt.pdb
// NameConform T0140.try11-try9
// ReadConformPDB decoys/T0140.try10-opt.pdb
// NameConform T0140.try11-try10
// ReadConformPDB decoys/T0140.try9-try8-15.37.80.pdb
// NameConform T0140.try11-try9-37

// ReadConformPDB decoys/T0140.try10-opt.pdb
// NameConform T0140.try12-try10
// ReadConformPDB decoys/T0140.try10.28.80.pdb
// NameConform T0140.try12-try10-28
// ReadConformPDB decoys/T0140.try11.30.90.pdb
// NameConform T0140.try12-try11-30
// ReadConformPDB decoys/T0140.try11.21.90.pdb
// NameConform T0140.try12-try11-21
// ReadConformPDB decoys/T0140.try11-opt.pdb
// NameConform T0140.try12-try11
// ReadConformPDB decoys/T0140.try11.10.90.pdb
// NameConform T0140.try12-try11-10

// ReadConformPDB decoys/T0140.try12.7.90.pdb
// NameConform T0140.try13-try12-7
// ReadConformPDB decoys/T0140.try12.5.90.pdb
// NameConform T0140.try13-try12-5
// ReadConformPDB decoys/T0140.try12.28.90.pdb
// NameConform T0140.try13-try12-28
// ReadConformPDB decoys/T0140.try12.15.90.pdb
// NameConform T0140.try13-try12-15
// ReadConformPDB decoys/T0140.try12-try11-30.27.90.pdb
// NameConform T0140.try13-try12-27

ReadConformPDB decoys/T0140.try9-try8-15.11.80.pdb	
  NameConform T0140.try14-try9-11
ReadConformPDB decoys/T0140.try13.15.80.pdb
  NameConform T0140.try14-try13-15
ReadConformPDB decoys/T0140.try13.7.80.pdb
  NameConform T0140.try14-try13-7
ReadConformPDB decoys/T0140.try10-opt.pdb
  NameConform T0140.try14-try10
ReadConformPDB decoys/T0140.try10.28.80.pdb
  NameConform T0140.try14-try10-28


ReportCost undertaker-try14.rdb

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0140.try14-al2
// PrintConformPDB T0140.try14-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0140.try14-al4
// PrintConformPDB T0140.try14-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0140.try14-al6
// PrintConformPDB T0140.try14-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0140.try14-al8
//  PrintConformPDB T0140.try14-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0140.try14-al10
//  PrintConformPDB T0140.try14-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0140.try14-al12
//  PrintConformPDB T0140.try14-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 T0140.t2k.frag

OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time


InitMethodProbs InsertAlignment 0.1 \
	ClashingRotamer 0.5 \
	InsertFragment 2 \
	CrossAndInsert 3 \
	CrossOver 0 \
	TwoFragment 1 \
	InsertSpecificFragment 4 \
	ReduceBreak 1 \
	CloseGap 0.5 \
	OptSubtree 0.04 \
	JiggleSubtree 0.03 \
	ReduceClash 0.5 \
	InsertSSBond 0

NameConform T0140.try14
OptConform pool_size 70 num_gen 80 gen_size 180 super_iter 20 pdb \
	use_all scwrl_each
NameConform T0140.try14-opt
PrintConformPDB T0140.try14-opt.pdb edges

SCWRLConform
NameConform T0140.try14-opt-scwrl
PrintConformPDB T0140.try14-opt-scwrl.pdb
CostConform
Time

quit