// 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.try46-opt.pdb
//NameConform T0129.try49-try46

//ReadConformPDB decoys/T0129.try47-opt.pdb
//NameConform T0129.try49-try47

//ReadConformPDB decoys/T0129.try43.8.50.pdb
//NameConform T0129.try49-try43

//ReadConformPDB decoys/T0129.try25-opt.pdb
//NameConform T0129.try49-try25

//ReadConformPDB decoys/T0129.try45-try43-3.8.50.pdb
//NameConform T0129.try49-try45

// ReadConformPDB decoys/T0129.try49-try48.12.20.pdb
// NameConform T0129.try50-try49


ReadConformPDB decoys/T0129.try48-try46.4.20.pdb	
    NameConform T0129.try51-try48
ReadConformPDB decoys/T0129.try47-opt.pdb
    NameConform T0129.try51-try47
ReadConformPDB decoys/T0129.try46-opt.pdb
    NameConform T0129.try51-try46
ReadConformPDB decoys/T0129.try45-try43-3.8.50.pdb
    NameConform T0129.try51-try45
ReadConformPDB decoys/T0129.try43.3.50.pdb
    NameConform T0129.try51-try43
ReadConformPDB decoys/T0129.try42.1.40.pdb	
    NameConform T0129.try51-try42
ReadConformPDB decoys/T0129.try41-opt.pdb
    NameConform T0129.try51-try41
ReadConformPDB decoys/T0129.try40-opt-scwrl.pdb
    NameConform T0129.try51-try40
ReadConformPDB decoys/T0129.try39-opt-scwrl.pdb
    NameConform T0129.try51-try39
ReadConformPDB decoys/T0129.try38-opt-scwrl.pdb
    NameConform T0129.try51-try38
ReadConformPDB decoys/T0129.try37-opt-scwrl.pdb
    NameConform T0129.try51-try37
ReadConformPDB decoys/T0129.try36-opt-scwrl.pdb
    NameConform T0129.try51-try36
ReadConformPDB decoys/T0129.try33-opt.pdb
    NameConform T0129.try51-try33
ReadConformPDB decoys/T0129.try49-try48.12.20.pdb
 NameConform T0129.try51-try49
ReadConformPDB decoys/T0129.try50.3.100.pdb
    NameConfrom T0129.try51-try50



CostConform
Time

ReportCost undertaker-try51.rdb

infileprefix	1ile/
    include read-alignments.under 
infileprefix	1htjF/
    include read-alignments.under 
infileprefix	1brwA/
    include read-alignments.under 


// TryAllAlign shrink 0.4 min_keep_length 5 
// TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0129.try49-al2
// PrintConformPDB T0129.try49-al2.pdb 
 
// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
// NameConform T0129.try49-al4
// PrintConformPDB T0129.try49-al4.pdb 
 
// TryAllAlign shrink 0.3 min_keep_length 4 
// TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0129.try49-al6
// PrintConformPDB T0129.try49-al6.pdb 
 
// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
// NameConform T0129.try49-al8
// PrintConformPDB T0129.try49-al8.pdb 

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0129.try49-al10
// PrintConformPDB T0129.try49-al10.pdb 

// CostConform
// Time


InFilePrefix 
ReadFragmentAlignment T0129.t2k.frag

OutFilePrefix
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/


InitMethodProbs InsertAlignment 0 \
	ClashingRotamer 0.5 \
	OneRotamer 0.4 \
	InsertFragment 10 \
	CrossAndInsert 4 \
        TwoFragment 1\
	CrossOver 0\
	InsertSpecificFragment 4 \
	ReduceBreak 1 \
	CloseGap 0.5 \
	JiggleSubtree 0.02 \
	OptSubtree 0.03 \
	ReduceClash 1 \
        ReduceConstraint 0 \
	InsertSSBond 0

NameConform T0129.try51
OptConform pool_size 40 num_gen 80 gen_size 150 super_iter 2 pdb \
	use_all scwrl_each

NameConform T0129.try51-opt
PrintConformPDB T0129.try51-opt.pdb

SCWRLConform
NameConform T0129.try51-opt-scwrl
PrintConformPDB T0129.try51-opt-scwrl.pdb

CostConform
Time

quit