// To be run from pce/casp5/t0180

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0180.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0180.t2k.undertaker-align.script 
ReadFragmentAlignment T0180.t2k-2track-undertaker.a2m

Time

ReportCost undertaker-try4.rdb

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0180.try4-al2
// PrintConformPDB T0180.try4-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0180.try4-al4
// PrintConformPDB T0180.try4-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0180.try4-al6
// PrintConformPDB T0180.try4-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0180.try4-al8
//  PrintConformPDB T0180.try4-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0180.try4-al10
//  PrintConformPDB T0180.try4-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0180.try4-al12
//  PrintConformPDB T0180.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 T0180.t2k.frag

InfilePrefix	1d2zA/
    include read-alignments.under 
InfilePrefix	1bx1A/
    include read-alignments.under 
InfilePrefix	1bx0A/
    include read-alignments.under 
InfilePrefix	1frqA/
    include read-alignments.under 
InfilePrefix	1qqfA/
    include read-alignments.under 
InfilePrefix	1i7pA/
    include read-alignments.under 
InfilePrefix	1frn/
    include read-alignments.under 
InfilePrefix	1g2nA/
    include read-alignments.under 
InfilePrefix	1b1zA/
    include read-alignments.under 
InfilePrefix	1l0yD/
    include read-alignments.under 

InfilePrefix


// 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 3 \
	CrossOver 0 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 5 \
	ReduceBreak 1 \
	CloseGap 0.1 \
	ReduceClash 1 \
	JiggleSubtree 0.1 \
	OptSubtree 0.1 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0180.try4
OptConform pool_size 40 num_gen 120 gen_size 180 super_iter 100 \
	use_all scwrl_each pdb
NameConform T0180.try4-opt
PrintConformPDB T0180.try4-opt.pdb edges
SCWRLConform
NameConform T0180.try4-opt-scwrl
PrintConformPDB T0180.try4-opt-scwrl.pdb

CostConform
Time

quit