// 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

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

InfilePrefix

Time

//ReadConformPDB robetta1.pdb
//     NameConform T0174.try14-robetta1
//ReadConformPDB robetta2.pdb
//     NameConform T0174.try14-robetta2
//ReadConformPDB robetta3.pdb
//     NameConform T0174.try14-robetta3
//ReadConformPDB robetta4.pdb
//     NameConform T0174.try14-robetta4
//ReadConformPDB robetta5.pdb
//     NameConform T0174.try14-robetta5

ReadConformPDB decoys/T0174.try9.4.20.pdb
     NameConform T0174.try14-try9.4

ReportCost undertaker-try14.rdb

//TryAllAlign shrink 0.4 min_keep_length 5 
//TryAllAlign shrink 0.4 min_keep_length 5 cumulative
//NameConform T0174.try14-al2
//PrintConformPDB T0174.try14-al2.pdb edges

//TryAllAlign shrink 0. min_keep_length 1 
//TryAllAlign shrink 0. min_keep_length 1 cumulative
//NameConform T0174.try14-al4
//PrintConformPDB T0174.try14-al4.pdb edges

//TryAllAlign shrink 0.3 min_keep_length 4 
//TryAllAlign shrink 0.3 min_keep_length 4 cumulative
//NameConform T0174.try14-al6
//PrintConformPDB T0174.try14-al6.pdb edges

//TryAllAlign shrink 0.1 min_keep_length 2 
//TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//NameConform T0174.try14-al8
//PrintConformPDB T0174.try14-al8.pdb edges

//TryAllAlign shrink 0.2 min_keep_length 3
//TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//NameConform T0174.try14-al10
//PrintConformPDB T0174.try14-al10.pdb edges

//TryAllAlign shrink 0. min_keep_length 1 
//TryAllAlign shrink 0. min_keep_length 1 cumulative
//NameConform T0174.try14-al12
//PrintConformPDB T0174.try14-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

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



// 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 10 \
	TwoFragment 10 \
	InsertSpecificFragment 5 \
	ReduceBreak 5 \
	CloseGap 0.1 \
	ReduceClash 1 \
	JiggleSubtree 0.03 \
	OptSubtree 0.03 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0174.try14
OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 1 \
	no_initial_fill use_all scwrl_each pdb
NameConform T0174.try14-opt
PrintConformPDB T0174.try14-opt.pdb edges
SCWRLConform
NameConform T0174.try14-opt-scwrl
PrintConformPDB T0174.try14-opt-scwrl.pdb

CostConform
Time

quit