// To be run from pce/casp5/t0187

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0187.rand
Time


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0187.t2k.undertaker-align.script 
ReadFragmentAlignment T0187.t2k-2track-undertaker.a2m

InfilePrefix 2pgi/
   include read-alignments.under
InfilePrefix 1bouB/
   include read-alignments.under
InfilePrefix 1gt8D/
   include read-alignments.under
InfilePrefix 1gthB/
   include read-alignments.under
InfilePrefix 1gteD/
   include read-alignments.under
InfilePrefix 1qopA/
   include read-alignments.under
InfilePrefix 1gthC/
   include read-alignments.under
InfilePrefix 1h7xB/
   include read-alignments.under
InfilePrefix 1h7wD/
   include read-alignments.under
InfilePrefix 1srvA/
   include read-alignments.under

InfilePrefix

Time

ReportCost undertaker-try1.rdb

 TryAllAlign shrink 0.4 min_keep_length 5 
 TryAllAlign shrink 0.4 min_keep_length 5 cumulative
NameConform T0187.try1-al2
PrintConformPDB T0187.try1-al2.pdb edges

TryAllAlign shrink 0. min_keep_length 1 
TryAllAlign shrink 0. min_keep_length 1 cumulative
NameConform T0187.try1-al4
PrintConformPDB T0187.try1-al4.pdb edges

 TryAllAlign shrink 0.3 min_keep_length 4 
 TryAllAlign shrink 0.3 min_keep_length 4 cumulative
NameConform T0187.try1-al6
PrintConformPDB T0187.try1-al6.pdb edges

TryAllAlign shrink 0.1 min_keep_length 2 
TryAllAlign shrink 0.1 min_keep_length 2 cumulative
 NameConform T0187.try1-al8
 PrintConformPDB T0187.try1-al8.pdb edges

TryAllAlign shrink 0.2 min_keep_length 3
TryAllAlign shrink 0.2 min_keep_length 3 cumulative
 NameConform T0187.try1-al10
 PrintConformPDB T0187.try1-al10.pdb edges

 TryAllAlign shrink 0. min_keep_length 1 
 TryAllAlign shrink 0. min_keep_length 1 cumulative
 NameConform T0187.try1-al12
 PrintConformPDB T0187.try1-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 T0187.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 \
	JiggleSubtree 0.03 \
	OptSubtree 0.03 \
	InsertSSBond 0 \
	ImproveSSBond 0
	
NameConform T0187.try1
OptConform pool_size 40 num_gen 60 gen_size 180 super_iter 20 pdb
NameConform T0187.try1-opt
PrintConformPDB T0187.try1-opt.pdb edges
SCWRLConform
NameConform T0187.try1-opt-scwrl
PrintConformPDB T0187.try1-opt-scwrl.pdb

CostConform
Time

quit