// To be run from pce/casp5/t0165

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

InfilePrefix

Time

// ReadConformPDB decoys/T0165.try1-opt-scwrl.pdb
//     NameConform T0165.try2-try1

// ReadConformPDB decoys/T0165.try2-opt.pdb
//    NameConform T0165.try4-try2
// ReadConformPDB decoys/T0165.try3-opt.pdb
//    NameConform T0165.try4-try3

ReadFragmentAlignment T0165-1c4xA.vast-hand.a2m

// ReadConformPDB decoys/T0165.try5-opt.pdb
//     NameConform T0165.try6-try5
// ReadConformPDB decoys/T0165.try4-opt.pdb
//     NameConform T0165.try6-try4
// ReadConformPDB decoys/T0165.try4-try2.0.60.pdb
//    NameConform T0165.try6-try4-0

// ReadConformPDB decoys/T0165-moved7.pdb
//    NameConform T0165.try8-moved

// ReadConformPDB decoys/T0165-moved7.pdb
//     NameConform T0165.try9-moved
// ReadConformPDB decoys/T0165.try8-opt-scwrl.pdb
//     NameConform T0165.try9-try8

// ReadConformPDB decoys/T0165-moved9.pdb
//    NameConform T0165.try10-moved

// ReadConformPDB decoys/T0165.try10-opt.pdb
//    NameConform T0165.try11-try10

ReadConformPDB decoys/T0165.try10-opt.pdb
    NameConform T0165.try12-try10
ReadConformPDB decoys/T0165.try11-opt.pdb
    NameConform T0165.try12-try11

ReportCost undertaker-try12.rdb

//   ConformFromSeq replace
//     NameConform T0165.rand

//   TryAllAlign shrink 0.4 min_keep_length 5 
//   TryAllAlign shrink 0.4 min_keep_length 5 cumulative
//  NameConform T0165.try12-al2
//  PrintConformPDB T0165.try12-al2.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0165.try12-al4
//  PrintConformPDB T0165.try12-al4.pdb edges

//   TryAllAlign shrink 0.3 min_keep_length 4 
//   TryAllAlign shrink 0.3 min_keep_length 4 cumulative
//  NameConform T0165.try12-al6
//  PrintConformPDB T0165.try12-al6.pdb edges

//  TryAllAlign shrink 0.1 min_keep_length 2 
//  TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//   NameConform T0165.try12-al8
//   PrintConformPDB T0165.try12-al8.pdb edges

//  TryAllAlign shrink 0.2 min_keep_length 3
//  TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//   NameConform T0165.try12-al10
//   PrintConformPDB T0165.try12-al10.pdb edges

//   TryAllAlign shrink 0. min_keep_length 1 
//   TryAllAlign shrink 0. min_keep_length 1 cumulative
//   NameConform T0165.try12-al12
//   PrintConformPDB T0165.try12-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 T0165.t2k.frag
ReadFragmentAlignment t0165-1-60/T0165.t2k.frag

Include T0165.t2k.undertaker-align.script 
ReadFragmentAlignment T0165.t2k-2track-undertaker.a2m

InfilePrefix 1a88A/
  include read-alignments.under
InfilePrefix 1a8s/
  include read-alignments.under
InfilePrefix 1jfrA/
  include read-alignments.under
InfilePrefix 1a8q/
  include read-alignments.under
InfilePrefix 1brt/
  include read-alignments.under
InfilePrefix 1broA/
  include read-alignments.under
InfilePrefix 1qfmA/
  include read-alignments.under
InfilePrefix 1din/
  include read-alignments.under
InfilePrefix 1c4xA/
  include read-alignments.under
InfilePrefix 1aurA/
  include read-alignments.under


Infileprefix	t0165-1-60/1i7xB/
    include read-alignments.under 
Infileprefix	t0165-1-60/1idm/
    include read-alignments.under 
Infileprefix	t0165-1-60/1ipd/
    include read-alignments.under 
Infileprefix	t0165-1-60/1dr8B/
    include read-alignments.under 
Infileprefix	t0165-1-60/1k9iD/
    include read-alignments.under 
Infileprefix	t0165-1-60/1f8vD/
    include read-alignments.under 
Infileprefix	t0165-1-60/1lnrO/
    include read-alignments.under 
Infileprefix	t0165-1-60/1ezrA/
    include read-alignments.under 
Infileprefix	t0165-1-60/1walA/
    include read-alignments.under 
Infileprefix	t0165-1-60/1gc9A/
    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 0.1 \
	OneRotamer 0.05 \
	ClashingRotamer 1 \
	InsertFragment 15 \
	CrossAndInsert 2 \
	TwoFragment 1 \
	InsertSpecificFragment 4 \
	ReduceBreak 10 \
	CloseGap 0.5 \
	ReduceClash 1 \
	JiggleSubtree 0.03 \
	OptSubtree 0.02 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0165.try12
OptConform pool_size 40 num_gen 70 gen_size 150 super_iter 2 \
	pdb use_all scwrl_each 
	// no_initial_fill
NameConform T0165.try12-opt
PrintConformPDB T0165.try12-opt.pdb edges
SCWRLConform
NameConform T0165.try12-opt-scwrl
PrintConformPDB T0165.try12-opt-scwrl.pdb

CostConform
Time

quit