// To be run from pce/casp5/t0174

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

//ConformFromSeq	replace // get a random conformation, removing all-zero one
//NameConform T0174.rand
//Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

//Include T0174.t2k.undertaker-align.script 
//ReadFragmentAlignment T0174.t2k-2track-undertaker.a2m

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

InfilePrefix

Time

// ReadConformPDB robetta1.pdb
//     NameConform T0174.try2-robetta1
// ReadConformPDB robetta2.pdb
//     NameConform T0174.try2-robetta2
// ReadConformPDB robetta3.pdb
//     NameConform T0174.try2-robetta3
// ReadConformPDB robetta4.pdb
//     NameConform T0174.try2-robetta4
// ReadConformPDB robetta5.pdb
//     NameConform T0174.try2-robetta5

//ReadConformPDB decoys/T0174.try2-opt-scwrl.pdb
//    NameConform T0174.jtry16-try2

//use j12-opt with strandZ rotated into the right position 
ReadConformPDB decoys/T0174.jtry12-rot5.pdb
	NameConform T0174.try16-jtry12


ReportCost undertaker-jtry16.rdb

// TryAllAlign shrink 0.4 min_keep_length 5 
// TryAllAlign shrink 0.4 min_keep_length 5 cumulative
//NameConform T0174.jtry16-al2
//PrintConformPDB T0174.jtry16-al2.pdb edges

//TryAllAlign shrink 0. min_keep_length 1 
//TryAllAlign shrink 0. min_keep_length 1 cumulative
//NameConform T0174.jtry16-al4
//PrintConformPDB T0174.jtry16-al4.pdb edges

// TryAllAlign shrink 0.3 min_keep_length 4 
// TryAllAlign shrink 0.3 min_keep_length 4 cumulative
//NameConform T0174.jtry16-al6
//PrintConformPDB T0174.jtry16-al6.pdb edges

//TryAllAlign shrink 0.1 min_keep_length 2 
//TryAllAlign shrink 0.1 min_keep_length 2 cumulative
// NameConform T0174.jtry16-al8
// PrintConformPDB T0174.jtry16-al8.pdb edges

//TryAllAlign shrink 0.2 min_keep_length 3
//TryAllAlign shrink 0.2 min_keep_length 3 cumulative
// NameConform T0174.jtry16-al10
// PrintConformPDB T0174.jtry16-al10.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0174.jtry16-al12
// PrintConformPDB T0174.jtry16-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 T0174.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 \
	ClashingRotamer 0.5 \
	OneRotamer 0.01 \
	InsertFragment 10 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 5 \
	ReduceBreak 0.5 \
	CloseGap 0.1 \
	ReduceClash 0.5\
	JiggleSubtree 0.5 \
	OptSubtree 0.5 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0174.jtry16
OptConform pool_size 40 num_gen 80 gen_size 180 super_iter 10 \
	no_initial_fill use_all scwrl_each pdb
NameConform T0174.jtry16-opt
PrintConformPDB T0174.jtry16-opt.pdb edges
SCWRLConform
NameConform T0174.jtry16-opt-scwrl
PrintConformPDB T0174.jtry16-opt-scwrl.pdb

CostConform
Time

quit