// To be run from pce/casp5/t0178

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0178.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

ReadFragmentAlignment T0178-1jclA-vast.a2m

Time

ReadConformPDB decoys/oops-T0178.try4-opt-scwrl.pdb
    NameConform T0178.try5-try4-o
ReadConformPDB decoys/T0178.try4-opt-scwrl.pdb
    NameConform T0178.try5-try4
ReadConformPDB decoys/T0178.try3-opt-scwrl.pdb
    NameConform T0178.try5-try3


ReportCost undertaker-try5.rdb

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0178.try5-al2
// PrintConformPDB T0178.try5-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0178.try5-al4
// PrintConformPDB T0178.try5-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0178.try5-al6
// PrintConformPDB T0178.try5-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0178.try5-al8
//  PrintConformPDB T0178.try5-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0178.try5-al10
//  PrintConformPDB T0178.try5-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0178.try5-al12
//  PrintConformPDB T0178.try5-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 T0178.t2k.frag

Include T0178.t2k.undertaker-align.script 
ReadFragmentAlignment T0178.t2k-2track-undertaker.a2m

ReadConformPDB decoys/T0178.try1-opt-scwrl.pdb
NameConform T0178.try5-try1

ReadConformPDB decoys/T0178.try2-opt-scwrl.pdb
NameConform T0178.try5-try2

ReadConformPDB decoys/T0178.try4-opt-scwrl.pdb
NameConform T0178.try5-try4

InfilePrefix 1jcjA/
   include read-alignments.under
InfilePrefix 1jclA/
   include read-alignments.under
InfilePrefix 1d3hA/
   include read-alignments.under
InfilePrefix 1d3gA/
   include read-alignments.under
InfilePrefix 1gthC/
   include read-alignments.under
InfilePrefix 1zfjA/
   include read-alignments.under
InfilePrefix 1gthB/
   include read-alignments.under
InfilePrefix 1gox/
   include read-alignments.under
InfilePrefix 1ep3A/
   include read-alignments.under
InfilePrefix 1qcwA/
   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 1 \
	ClashingRotamer 1 \
	OneRotamer 0.2 \
	InsertFragment 8 \
	CrossOver 0 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 10 \
	ReduceBreak 1 \
	CloseGap 0.1 \
	ReduceClash 1 \
	JiggleSubtree 0.03 \
	OptSubtree 0.05 \ 
	InsertSSBond 0 \
	ImproveSSBond 0.5
	
NameConform T0178.try5
OptConform pool_size 40 num_gen 120 gen_size 200 super_iter 15 pdb
NameConform T0178.try5-opt
PrintConformPDB T0178.try5-opt.pdb edges
SCWRLConform
NameConform T0178.try5-opt-scwrl
PrintConformPDB T0178.try5-opt-scwrl.pdb

CostConform
Time

quit