// To be run from pce/casp5/t0147_twice

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0147_twice.rand
Time


InFilePrefix 
Include T0147_twice.t2k.undertaker-align.script 
ReadFragmentAlignment T0147_twice.t2k-2track-undertaker.a2m

Time

ReportCost undertaker-try1.rdb

  TryAllAlign shrink 0.4 min_keep_length 5 
  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
 NameConform T0147_twice.al2
 PrintConformPDB T0147_twice.try1-al2.pdb edges
 
 TryAllAlign shrink 0. min_keep_length 1 
 TryAllAlign shrink 0. min_keep_length 1 cumulative
 NameConform T0147_twice.try1-al4
 PrintConformPDB T0147_twice.try1-al4.pdb edges
 
  TryAllAlign shrink 0.3 min_keep_length 4 
  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
 NameConform T0147_twice.try1-al6
 PrintConformPDB T0147_twice.try1-al6.pdb edges
 
 TryAllAlign shrink 0.1 min_keep_length 2 
 TryAllAlign shrink 0.1 min_keep_length 2 cumulative
  NameConform T0147_twice.try1-al8
  PrintConformPDB T0147_twice.try1-al8.pdb edges
 
 TryAllAlign shrink 0.2 min_keep_length 3
 TryAllAlign shrink 0.2 min_keep_length 3 cumulative
  NameConform T0147_twice.try1-al10
  PrintConformPDB T0147_twice.try1-al10.pdb edges
 
  TryAllAlign shrink 0. min_keep_length 1 
  TryAllAlign shrink 0. min_keep_length 1 cumulative
  NameConform T0147_twice.try1-al12
  PrintConformPDB T0147_twice.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 fragment-a2m/
// Include read-fragments.script
ReadFragmentAlignment T0147_twice.t2k.frag
InFilePrefix 

Time



InitMethodProbs InsertAlignment 0.1 \
	ClashingRotamer 0.5 \
	InsertFragment 1 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 0.5 \
	ReduceBreak 5 \
	CloseGap 0.01 \
	ReduceClash 1 \
	InsertSSBond 0

NameConform T0147_twice.try1
OptConform pool_size 40 num_gen 20 gen_size 120 super_iter 20 pdb
NameConform T0147_twice.try1-opt
PrintConformPDB T0147_twice.try1-opt.pdb edges
CostConform
Time

quit