// To be run from pce/casp5/t0167

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/


InFilePrefix 
ReadTemplateAtoms Template.atoms

ReadFragmentAlignment T0167-1jeoA.vast.a2m

Time

// ReadConformPDB decoys/T0167.try1-opt-scwrl.pdb
// NameConform T0167.try2-try1

ReadConformPDB decoys/T0167.try3-opt.pdb
   Nameconform T0167.try4-try4
   

ReportCost undertaker-try4.rdb

// ConformFromSeq	replace // get a random conformation, removing all-zero one
// NameConform T0167.rand
Time

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0167.try4-al2
// PrintConformPDB T0167.try4-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0167.try4-al4
// PrintConformPDB T0167.try4-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0167.try4-al6
// PrintConformPDB T0167.try4-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0167.try4-al8
//  PrintConformPDB T0167.try4-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0167.try4-al10
//  PrintConformPDB T0167.try4-al10.pdb edges

 TryAllAlign shrink 0. min_keep_length 1 
 TryAllAlign shrink 0. min_keep_length 1 cumulative
 NameConform T0167.try4-al12
 PrintConformPDB T0167.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 T0167.t2k.frag
Include T0167.t2k.undertaker-align.script 
ReadFragmentAlignment T0167.t2k-2track-undertaker.a2m

InfilePrefix 1jeoA/
  include read-alignments.under
InfilePrefix 1moq/
  include read-alignments.under
InfilePrefix 1jxaA/
  include read-alignments.under
InfilePrefix 2pgi/
  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 \
	ClashingRotamer 1 \
	OneRotamer 1 \
	InsertFragment 10 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 4 \
	ReduceBreak 2 \
	CloseGap 0.1 \
	ReduceClash 1 \
	JiggleSubtree 0.03 \
	OptSubtree 0.03 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0167.try4
OptConform pool_size 60 num_gen 120 gen_size 200 super_iter 10 \
	use_all scwrl_each pdb
NameConform T0167.try4-opt
PrintConformPDB T0167.try4-opt.pdb edges
SCWRLConform
NameConform T0167.try4-opt-scwrl
PrintConformPDB T0167.try4-opt-scwrl.pdb

CostConform
Time

quit