SetSeed

InfilePrefix 
Include define-score.under

// Note: keep the random conformation created in define-score

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

InFilePrefix 
ReadTemplateAtoms Template.atoms

Include YGR030C.t2k.undertaker-align.under 
ReadFragmentAlignment YGR030C.t2k-2track-undertaker.a2m

// InfilePrefix 1xxxX/
//   include read-alignments.under

InfilePrefix

Time

ReportCost undertaker-try1.rdb

TryAllAlign shrink 0.4 min_keep_length 5 
TryAllAlign shrink 0.4 min_keep_length 5 cumulative
NameConform YGR030C.try1-al2
PrintConformPDB YGR030C.try1-al2.pdb edges

TryAllAlign shrink 0. min_keep_length 1 
TryAllAlign shrink 0. min_keep_length 1 cumulative
NameConform YGR030C.try1-al4
PrintConformPDB YGR030C.try1-al4.pdb edges

TryAllAlign shrink 0.3 min_keep_length 4 
TryAllAlign shrink 0.3 min_keep_length 4 cumulative
NameConform YGR030C.try1-al6
PrintConformPDB YGR030C.try1-al6.pdb edges

TryAllAlign shrink 0.1 min_keep_length 2 
TryAllAlign shrink 0.1 min_keep_length 2 cumulative
NameConform YGR030C.try1-al8
PrintConformPDB YGR030C.try1-al8.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 YGR030C.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 0.3 \
	OneRotamer 0.01 \
	ClashingRotamer 0.5 \
	InsertFragment 10 \
	CrossOver 0 \
	CrossAndInsert 5 \
	TwoFragment 10 \
	InsertSpecificFragment 5 \
	ReduceBreak 5 \
	CloseGap 0.1 \
	ReduceClash 1 \
	JiggleSubtree 0.03 \
	OptSubtree 0.03 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform YGR030C.try1
OptConform pool_size 40 num_gen 60 gen_size 180 super_iter 10 pdb \
	scwrl_each use_all
NameConform YGR030C.try1-opt
PrintConformPDB YGR030C.try1-opt.pdb edges
SCWRLConform
NameConform YGR030C.try1-opt-scwrl
PrintConformPDB YGR030C.try1-opt-scwrl.pdb

CostConform
Time

quit