// To be run from pce/casp5/t0160

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0160.t2k.undertaker-align.script 
ReadFragmentAlignment T0160.t2k-2track-undertaker.a2m

InFilePrefix 1mspA/
Include read-alignments.under

InFilePrefix 1grwA/
Include read-alignments.under

InFilePrefix 2mspA/
Include read-alignments.under

InFilePrefix

// ReadConformPDB decoys/T0160.try1-opt.pdb

Time

// ReadConformPDB decoys/T0160.try3-opt.pdb
//  NameConform T0160.try4-try3
// ReadConformPDB decoys/T0160.try3-opt-scwrl.pdb
//  NameConform T0160.try4-try3-s

// ReadConformPDB decoys/T0160.try3-opt-scwrl.pdb
//  NameConform T0160.try5-try3-s
// ReadConformPDB decoys/T0160.try4-opt.pdb
//  NameConform T0160.try5-try4

ReadConformPDB decoys/T0160.try5-opt.pdb
  NameConform T0160.try6-try5
ReadConformPDB decoys/T0160.try5.0.100.pdb
  NameConform T0160.try6-try5-0
ReadConformPDB decoys/T0160.try5.3.100.pdb
  NameConform T0160.try6-try5-3
ReadConformPDB decoys/T0160.try5.7.100.pdb
  NameConform T0160.try6-try5-7
ReadConformPDB decoys/T0160.try5.5.100.pdb
  NameConform T0160.try6-try5-5

ReportCost undertaker-try6.rdb

// ConformFromSeq	replace // get a random conformation, removing all-zero one
// NameConform T0160.rand
// Time


//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0160.try6-al2
// PrintConformPDB T0160.try6-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0160.try6-al4
// PrintConformPDB T0160.try6-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0160.try6-al6
// PrintConformPDB T0160.try6-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0160.try6-al8
//  PrintConformPDB T0160.try6-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0160.try6-al10
//  PrintConformPDB T0160.try6-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0160.try6-al12
//  PrintConformPDB T0160.try6-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.

ReadFragmentAlignment T0160.t2k.frag
InFilePrefix 

OutFilePrefix 
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 0.1 \
	OneRotamer 10 \
	ClashingRotamer 3 \
	InsertFragment 8 \
	Crossover 0 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 6 \
	ReduceBreak 5 \
	CloseGap 0.1 \
	OptSubtree 0.04 \
	JiggleSubtree 0.04 \
	ReduceClash 2 \
	ReduceConstraint 1\
	InsertSSBond 0 \
	ImproveSSBond 0

NameConform T0160.try6
OptConform pool_size 70 num_gen 40 gen_size 200 super_iter 10 \
	pdb use_all scwrl_each
NameConform T0160.try6-opt
PrintConformPDB T0160.try6-opt.pdb edges

SCWRLConform
NameConform  T0160.try6-opt-scwrl
PrintConformPDB T0160.try6-opt-scwrl.pdb 

CostConform
Time

quit