// To be run from pce/casp5/t0129

SetSeed

InfilePrefix
Include define-score.script

MakeGenericFragmentLibrary
Time


InfilePrefix
ReadTemplateAtoms Template.atoms

Include T0129-undertaker-align.script 

ReadFragmentAlignment T0129-t2k-2track-undertaker.a2m

// have now finished all the initial set up of libraries.
Time


OutFilePrefix decoys/

 ConformFromSeq	replace // get a random conformation, removing all-zero one
 NameConform T0129-rand

 InfilePrefix
// Include read-some-decoys-28.script
 InfilePrefix

PopConform	// get rid of random conformation


// ReadConformPDB robetta2.pdb
// NameConform try32-robetta2
// ReadConformPDB robetta3.pdb
// NameConform try32-robetta3
// ReadConformPDB robetta4.pdb
// NameConform try32-robetta4
// ReadConformPDB robetta5.pdb
// NameConform try32-robetta5
// ReadConformPDB robetta1.pdb
// NameConform try32-robetta1

// ReadConformPDB decoys/T0129-try17-opt.pdb
// NameConform T0129.try33-try17
// ReadConformPDB decoys/T0129.try32-opt-scwrl.pdb
// NameConform T0129.try33-try32

// ReadConformPDB decoys/T0129-try41-opt-moved.pdb
// NameConform T0129.try42

//ReadConformPDB decoys/T0129.try42-scwrl.10.40.pdb
//NameConform T0129.try44-try42-10
//ReadConformPDB decoys/T0129.try42.7.40.pdb
//NameConform T0129.try44-try42-7
//ReadConformPDB decoys/T0129.try42.1.40.pdb
//NameConform T0129.try44-try42-1

// ReadConformPDB decoys/T0129.try43-opt-scwrl.pdb
// NameConform T0129.try45-try43-1
// ReadConformPDB decoys/T0129.try43.3.50.pdb
// NameConform T0129.try45-try43-2
// ReadConformPDB decoys/T0129.try43.9.50.pdb
// NameConform T0129.try45-try43-3
// ReadConformPDB decoys/T0129.try43.6.50.pdb
// NameConform T0129.try45-try43-4

ReadConformPDB decoys/T0129.try45-try43-3.1.50.pdb
 NameConform T0129.try46-try45-1
ReadConformPDB decoys/T0129.try45-try43-2.4.50.pdb
 NameConform T0129.try46-try45-4
ReadConformPDB decoys/T0129.try45-try43-3.8.50.pdb
 NameConform T0129.try46-try45-8


CostConform
Time

ReportCost undertaker-try46.rdb


// TryAllAlign shrink 0.4 min_keep_length 5 
// TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0129.try44-al2
// PrintConformPDB T0129.try44-al2.pdb 
 
// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
// NameConform T0129.try44-al4
// PrintConformPDB T0129.try44-al4.pdb 
 
// TryAllAlign shrink 0.3 min_keep_length 4 
// TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0129.try44-al6
// PrintConformPDB T0129.try44-al6.pdb 
 
// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
// NameConform T0129.try44-al8
// PrintConformPDB T0129.try44-al8.pdb 

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0129.try44-al10
// PrintConformPDB T0129.try44-al10.pdb 

 CostConform
 Time


InFilePrefix 
ReadFragmentAlignment T0129.t2k.frag

OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/


InitMethodProbs InsertAlignment 0 \
	ClashingRotamer 0.5 \
	InsertFragment 11 \
	CrossAndInsert 1\
	CrossOver 0\
	OneRotamer 0.1 \
	InsertSpecificFragment 7 \
	ReduceBreak 5 \
	CloseGap 0.2 \
	JiggleSubtree 0.03 \
	OptSubtree 0.06 \
	ReduceClash 1 \
	InsertSSBond 0

NameConform T0129.try46
OptConform pool_size 40 num_gen 100 gen_size 200 super_iter 10 pdb \
	use_all scwrl_each no_initial_fill

NameConform T0129.try46-opt
PrintConformPDB T0129.try46-opt.pdb

SCWRLConform
NameConform T0129.try46-opt-scwrl
PrintConformPDB T0129.try46-opt-scwrl.pdb

CostConform
Time

quit