// To be run from pce/casp5/t0151

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0151.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0151.t2k.undertaker-align.script 
ReadFragmentAlignment T0151.t2k-2track-undertaker.a2m

InFilePrefix 1qvcA/
Include read-alignments.under
InFilePrefix 1kawA/
Include read-alignments.under
InFilePrefix 3ullA/
Include read-alignments.under
InFilePrefix 1eygA/
Include read-alignments.under

Time

// ReadConformPDB decoys/T0151.try2-opt-scwrl.pdb
// NameConform T0151.try3-try2

ReadConformPDB decoys/T0151.try3-opt.pdb
NameConform T0151.try4-try3
ReadConformPDB decoys/T0151.try3-try2.4.30.pdb
NameConform T0151.try4-try3-4
ReadConformPDB decoys/T0151.try3-al4.18.30.pdb
NameConform T0151.try4-try3-18

SCWRLConform
NameConform T0151.try4-try3-s

ReportCost undertaker-try4.rdb


//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0151.try4-al2
// PrintConformPDB T0151.try4-al2.pdb edges
 
// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0151.try4-al4
// PrintConformPDB T0151.try4-al4.pdb edges
 
//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0151.try4-al6
// PrintConformPDB T0151.try4-al6.pdb edges
 
// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0151.try4-al8
//  PrintConformPDB T0151.try4-al8.pdb edges
 
// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0151.try4-al10
//  PrintConformPDB T0151.try4-al10.pdb edges
 
//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0151.try4-al12
//  PrintConformPDB T0151.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 
ReadFragmentAlignment T0151.t2k.frag


OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 0.1 \
	ClashingRotamer 0.5 \
	InsertFragment 1 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 0.5 \
	ReduceBreak 5 \
	CloseGap 0.1 \
	OptSubtree 0.2 \
	JiggleSubtree 0.2 \
	ReduceClash 1 \
	InsertSSBond 0

NameConform T0151.try4
OptConform pool_size 60 num_gen 40 gen_size 170 super_iter 20 \
	pdb use_all scwrl_each
NameConform T0151.try4-opt
PrintConformPDB T0151.try4-opt.pdb edges

SCWRLConform
NameConform T0151.try4-opt-scwrl
PrintConformPDB T0151.try4-opt-scwrl.pdb 


CostConform
Time

quit