// To be run from pce/casp5/t0191

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0191.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

ReadFragmentAlignment	T0191-1gpjA.vast.a2m

// include try-alignments.under

InfilePrefix decoys/

// ReadConformPDB T0191-start.pdb
//    NameConform T0191.try1-start

InfilePrefix

Time

ReportCost undertaker-try3.rdb

TryAllAlign shrink 0.4 min_keep_length 5 
TryAllAlign shrink 0.4 min_keep_length 5 cumulative
NameConform T0191.try3-al2
PrintConformPDB T0191.try3-al2.pdb edges

TryAllAlign shrink 0. min_keep_length 1 
TryAllAlign shrink 0. min_keep_length 1 cumulative
NameConform T0191.try3-al4
PrintConformPDB T0191.try3-al4.pdb edges

TryAllAlign shrink 0.3 min_keep_length 4 
TryAllAlign shrink 0.3 min_keep_length 4 cumulative
NameConform T0191.try3-al6
PrintConformPDB T0191.try3-al6.pdb edges

TryAllAlign shrink 0.1 min_keep_length 2 
TryAllAlign shrink 0.1 min_keep_length 2 cumulative
NameConform T0191.try3-al8
PrintConformPDB T0191.try3-al8.pdb edges

TryAllAlign shrink 0.2 min_keep_length 3
TryAllAlign shrink 0.2 min_keep_length 3 cumulative
NameConform T0191.try3-al10
PrintConformPDB T0191.try3-al10.pdb edges

TryAllAlign shrink 0. min_keep_length 1 
TryAllAlign shrink 0. min_keep_length 1 cumulative
NameConform T0191.try3-al12
PrintConformPDB T0191.try3-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 T0191.t2k.frag
include try-alignments.under

// 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 0.5 \
	OneRotamer 0.01 \
	ClashingRotamer 0.5 \
	InsertFragment 5 \
	CrossAndInsert 5 \
	CrossOver 0 \
	TwoFragment 10 \
	InsertSpecificFragment 8 \
	ReduceBreak 1 \
	CloseGap 0.2 \
	ReduceClash 5 \
	ReduceConstraint 5 \
	JiggleSubtree 0.03 \
	OptSubtree 0.01 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0191.try3
OptConform pool_size 40 num_gen 200 gen_size 200 super_iter 1 \
	pdb use_all
	// scwrl_each
NameConform T0191.try3-opt
PrintConformPDB T0191.try3-opt.pdb edges
SCWRLConform
NameConform T0191.try3-opt-scwrl
PrintConformPDB T0191.try3-opt-scwrl.pdb

CostConform
Time

quit