// To be run from pce/casp5/t0163

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0163.t2k.undertaker-align.script 
ReadFragmentAlignment T0163.t2k-2track-undertaker.a2m

InFilePrefix 1el5A/
include read-alignments.under
InFilePrefix 1l9fA/
include read-alignments.under
InFilePrefix 1an9A/
include read-alignments.under
InFilePrefix 1aa8A/
include read-alignments.under
InFilePrefix 1c0pA/
include read-alignments.under
InFilePrefix 1eliA/
include read-alignments.under
InFilePrefix 1e39A/
include read-alignments.under

InFilePrefix
Time

// ReadConformPDB decoys/T0163.try2-opt-scwrl.pdb
// NameConform try3-try2

// ReadConformPDB decoys/T0163.try3-opt-scwrl.pdb
// NameConform try4-try3

//ReadConformPDB decoys/T0163.try5-opt-scwrl.pdb
//   NameConformt T0163.try6-try5

ReadConformPDB decoys/T0163.try6-opt.pdb
   NameConformt T0163.try7-try6

ReportCost undertaker-try7.rdb

//  ConformFromSeq	replace // get a random conformation, removing all-zero one
//  NameConform T0163.rand
//  Time

// TryAllAlign shrink 0.4 min_keep_length 5 
// TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0163.try7-al2
// PrintConformPDB T0163.try7-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0163.try7-al4
// PrintConformPDB T0163.try7-al4.pdb edges

// TryAllAlign shrink 0.3 min_keep_length 4 
// TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0163.try7-al6
// PrintConformPDB T0163.try7-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
// NameConform T0163.try7-al8
// PrintConformPDB T0163.try7-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
// NameConform T0163.try7-al10
// PrintConformPDB T0163.try7-al10.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0163.try7-al12
// PrintConformPDB T0163.try7-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 T0163.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 0.1 \
	ClashingRotamer 1 \
	InsertFragment 10 \
	CrossAndInsert 1 \
	CrossOver 0 \
	TwoFragment 1 \
	InsertSpecificFragment 5 \
	ReduceBreak 5 \
	CloseGap 0.2 \
	ReduceClash 1 \
	JiggleSubtree 0.04\
	OptSubtree 0.04 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0163.try7
OptConform pool_size 40 num_gen 50 gen_size 180 super_iter 10 \
	pdb scwrl_each use_all
NameConform T0163.try7-opt
PrintConformPDB T0163.try7-opt.pdb edges
SCWRLConform
NameConform T0163.try7-opt-scwrl
PrintConformPDB T0163.try7-opt-scwrl.pdb

CostConform
Time

quit