// To be run from pce/casp5/t0156

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0156.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0156.t2k.undertaker-align.script 
ReadFragmentAlignment T0156.t2k-2track-undertaker.a2m


Time

ReportCost undertaker-try4.rdb

 TryAllAlign shrink 0.4 min_keep_length 5 
 TryAllAlign shrink 0.4 min_keep_length 5 cumulative
NameConform T0156.try4-al2
PrintConformPDB T0156.try4-al2.pdb edges

TryAllAlign shrink 0. min_keep_length 1 
TryAllAlign shrink 0. min_keep_length 1 cumulative
NameConform T0156.try4-al4
PrintConformPDB T0156.try4-al4.pdb edges

 TryAllAlign shrink 0.3 min_keep_length 4 
 TryAllAlign shrink 0.3 min_keep_length 4 cumulative
NameConform T0156.try4-al6
PrintConformPDB T0156.try4-al6.pdb edges

TryAllAlign shrink 0.1 min_keep_length 2 
TryAllAlign shrink 0.1 min_keep_length 2 cumulative
 NameConform T0156.try4-al8
 PrintConformPDB T0156.try4-al8.pdb edges

TryAllAlign shrink 0.2 min_keep_length 3
TryAllAlign shrink 0.2 min_keep_length 3 cumulative
 NameConform T0156.try4-al10
 PrintConformPDB T0156.try4-al10.pdb edges

 TryAllAlign shrink 0. min_keep_length 1 
 TryAllAlign shrink 0. min_keep_length 1 cumulative
 NameConform T0156.try4-al12
 PrintConformPDB T0156.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 T0156.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 \
	ClashingRotamer 0.5 \
	InsertFragment 1 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 1.5 \
	ReduceBreak 5 \
	CloseGap 0.1 \
	ReduceClash 1 \
	InsertSSBond 0 \
    ImproveSSBond 0
	
NameConform T0156.try4
OptConform pool_size 40 num_gen 20 gen_size 120 super_iter 20 pdb
NameConform T0156.try4-opt
PrintConformPDB T0156.try4-opt.pdb edges
SCWRLConform
NameConform T0156.try4-opt-scwrl
PrintConformPDB T0156.try4-opt-scwrl.pdb

CostConform
Time

quit