// To be run from pce/casp5/t0152 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0152.rand Time InFilePrefix ReadTemplateAtoms Template.atoms ReadFragmentAlignment T0152-1bo4A.vast.fasta ReadFragmentAlignment T0152-1qsmD.vast.fasta Include T0152.t2k.undertaker-align.script ReadFragmentAlignment T0152.t2k-2track-undertaker.a2m InFilePrefix 1i21A/ include read-alignments.under InFilePrefix 1i12A/ include read-alignments.under InFilePrefix 1i1dA/ include read-alignments.under InFilePrefix 1cjwA/ include read-alignments.under InFilePrefix 1qsmA/ include read-alignments.under InFilePrefix 1bob/ include read-alignments.under InFilePrefix Time // ReadConformPDB decoys/T0152.try1-opt.pdb // NameConform T0152.try5-try1 // ReadConformPDB decoys/T0152.try5-opt-scwrl.pdb // NameConform T0152.try6-try5 //ReadConformPDB decoys/T0152.try7.0.40.pdb //NameConform T0152-try8-try7-0 //ReadConformPDB decoys/T0152.try7.1.40.pdb //NameConform T0152-try8-try7-1 //ReadConformPDB decoys/T0152.try7.3.40.pdb //NameConform T0152-try8-try7-3 //ReadConformPDB decoys/T0152.try7.4.40.pdb //NameConform T0152-try8-try7-4 //ReadConformPDB decoys/T0152.try7.5.40.pdb //NameConform T0152-try8-try7-5 //ReadConformPDB decoys/T0152.try7.6.40.pdb //NameConform T0152-try8-try7-6 //ReadConformPDB decoys/T0152.try6-opt.pdb //NameConform T0152-try12-try6 //ReadConformPDB decoys/T0152.try7.4.40.pdb //NameConform T0152-try12-try7-4 //ReadConformPDB decoys/T0152.try7.1.40.pdb //NameConform T0152-try12-try7-1 //ReadConformPDB decoys/T0152.try7.3.40.pdb //NameConform T0152-try12-try7-3 //ReadConformPDB decoys/T0152.try7.6.40.pdb //NameConform T0152-try12-try7-6 //ReadConformPDB decoys/T0152.try9-opt.pdb //NameConform T0152-try12-try9 //ReadConformPDB decoys/T0152.try8-opt.pdb //NameConform T0152-try12-try8 //ReadConformPDB decoys/T0152.try10-opt.pdb //NameConform T0152-try12-try8 // ReadConformPDB decoys/T0152.try13-opt-scwrl.pdb // NameConform T0152-try14-try13 // ReadConformPDB decoys/T0152.try12-al8.19.30.pdb // NameConform T0152-try14-try12-19 // ReadConformPDB decoys/T0152-try11-try8.2.30.pdb // NameConform T0152-try14-try11-2 // ReadConformPDB decoys/T0152.try7.3.40.pdb // NameConform T0152-try14-try7-3 //ReadConformPDB decoys/T0152.try13-opt.pdb //NameConform T0152-try16-try13 //ReadConformPDB decoys/T0152.try7.3.40.pdb //NameConform T0152-try16-try7-3 ReadConformPDB decoys/T0152.try15-opt.pdb NameConform T0152.try16-try15 ReportCost undertaker-try16.rdb TryAllAlign shrink 0.4 min_keep_length 5 TryAllAlign shrink 0.4 min_keep_length 5 cumulative NameConform T0152.try16-al2 PrintConformPDB T0152.try16-al2.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0152.try16-al4 PrintConformPDB T0152.try16-al4.pdb edges TryAllAlign shrink 0.3 min_keep_length 4 TryAllAlign shrink 0.3 min_keep_length 4 cumulative NameConform T0152.try16-al6 PrintConformPDB T0152.try16-al6.pdb edges TryAllAlign shrink 0.1 min_keep_length 2 TryAllAlign shrink 0.1 min_keep_length 2 cumulative NameConform T0152.try16-al8 PrintConformPDB T0152.try16-al8.pdb edges TryAllAlign shrink 0.2 min_keep_length 3 TryAllAlign shrink 0.2 min_keep_length 3 cumulative NameConform T0152.try16-al10 PrintConformPDB T0152.try16-al10.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0152.try16-al12 PrintConformPDB T0152.try16-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 T0152.t2k.frag OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0.2 \ ClashingRotamer 0.5 \ InsertFragment 3 \ CrossAndInsert 3 \ TwoFragment 1 \ InsertSpecificFragment 2.5 \ ReduceBreak 0.5 \ CloseGap 0.1 \ JiggleSubtree 0.02 \ OptSubtree 0.02 \ ReduceClash 1 \ InsertSSBond 0 NameConform T0152.try16 OptConform pool_size 70 num_gen 80 gen_size 180 super_iter 20 \ pdb scwrl_each use_all NameConform T0152.try16-opt PrintConformPDB T0152.try16-opt.pdb edges SCWRLConform NameConform T0152.try16-opt-scwrl PrintConformPDB T0152.try16-opt-scwrl.pdb edges CostConform Time quit