// To be run from pce/casp5/t0139 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0139.rand Time ReadTemplateAtoms Template.atoms // The following alignments are believed to be good: InFilePrefix Include T0139.undertaker-align.script ReadFragmentAlignment T0139.t2k-2track-undertaker.a2m Time // ReadConformPDB decoys/T0139.try5-opt.pdb // NameConform T0139.try6-try5 // ReadConformPDB decoys/T0139.try8-opt-scwrl.pdb // NameConform T0139.try12-try8 // // ReadConformPDB decoys/T0139.try9-opt-scwrl.pdb // NameConform T0139.try12-try9 // // ReadConformPDB decoys/T0139.try10-opt-scwrl.pdb // NameConform T0139.try12-try10 // // ReadConformPDB decoys/T0139.try11-opt.pdb // NameConform T0139.try12-try11 // // ReadConformPDB decoys/T0139.try11-opt-scwrl.pdb // NameConform T0139.try12-try11-scwrl // ReadConformPDB decoys/T0139.try10-opt-scwrl.pdb // NameConform T0139.try13-try10 // ReadConformPDB decoys/T0139.try11-opt.pdb // NameConform T0139.try13-try11 // ReadConformPDB decoys/T0139.try11-opt-scwrl.pdb // NameConform T0139.try13-try11-scwrl // ReadConformPDB decoys/T0139.try12-opt.pdb // NameConform T0139.try17-try12-scwrl // ReadConformPDB decoys/T0139.try14-opt.pdb // NameConform T0139.try17-try14-scwrl // ReadConformPDB decoys/T0139.try15-opt.pdb // NameConform T0139.try17-try15-scwrl // ReadConformPDB decoys/T0139.try16-opt.pdb // NameConform T0139.try17-try16-scwrl // ReadConformPDB decoys/T0139.try17-opt.pdb // NameConform T0139.try19-try17 // ReadConformPDB decoys/T0139.try18-opt.pdb // NameConform T0139.try19-try18 // ReadConformPDB decoys/T0139.try17-opt.pdb // NameConform T0139.try20-try17 // ReadConformPDB decoys/T0139.try18-opt.pdb // NameConform T0139.try20-try18 // ReadConformPDB decoys/T0139.try19-try17.24.80.pdb // NameConform T0139.try20-try19-24 // ReadConformPDB decoys/T0139.try19-try17.23.80.pdb // NameConform T0139.try20-try19-23 // ReadConformPDB decoys/T0139.try19-try17.25.80.pdb // NameConform T0139.try20-try19-25 // ReadConformPDB decoys/T0139.try19-try17.9.80.pdb // NameConform T0139.try20-try19-9 // ReadConformPDB decoys/T0139.try19-opt.pdb // NameConform T0139.try20-try19 // ReadConformPDB decoys/T0139.try20-opt.pdb // NameConform T0139.try21-try20 // ReadConformPDB robetta1.pdb // NameConform T0139.try21-rob1 // ReadConformPDB robetta2.pdb // NameConform T0139.try21-rob2 // ReadConformPDB robetta3.pdb // NameConform T0139.try21-rob3 // ReadConformPDB robetta4.pdb // NameConform T0139.try21-rob4 // ReadConformPDB robetta5.pdb // NameConform T0139.try21-rob5 // ReadConformPDB decoys/T0139.try20-try19-24.5.90.pdb // NameConform T0139.try21-try20-5 // ReadConformPDB decoys/T0139.try20-try19-9.0.90.pdb // NameConform T0139.try21-try20-0 // ReadConformPDB decoys/T0139.try20-try19-9.6.90.pdb // NameConform T0139.try21-try20-6 // ReadConformPDB decoys/T0139.try20-try19-25.3.90.pdb // NameConform T0139.try21-try20-3 // readconformPDB decoys/T0139.try21-opt-scwrl.pdb // NameConform T0139.try22-try21 // readconformPDB decoys/T0139.try21.0.90.pdb // NameConform T0139.try22-try21-0 // readconformPDB decoys/T0139.try21-opt-scwrl.pdb // NameConform T0139.try24-try21 // readconformPDB decoys/T0139.try21.0.90.pdb // NameConform T0139.try24-try21-0 // readconformPDB decoys/T0139.try3-opt.pdb // NameConform T0139.try25-try3 // readconformPDB decoys/T0139.try14-opt.pdb // NameConform T0139.try25-try14 // readconformPDB decoys/T0139.try18-opt.pdb // NameConform T0139.try25-try18 // readconformPDB decoys/T0139.try19-opt.pdb // NameConform T0139.try25-try19 // readconformPDB decoys/T0139.try20-opt.pdb // NameConform T0139.try25-try20 // readconformPDB decoys/T0139.try21-opt.pdb // NameConform T0139.try25-try21 // readconformPDB decoys/T0139.try22-opt.pdb // NameConform T0139.try25-try22 // readconformPDB decoys/T0139.try23-opt.pdb // NameConform T0139.try25-try23 // readconformPDB decoys/T0139.try24-opt.pdb // NameConform T0139.try25-try24 // readconformPDB decoys/T0139.try24.19.40.pdb // NameConform T0139.try25-try24-19 // readconformPDB decoys/T0139.try24.13.40.pdb // NameConform T0139.try25-try24-13 // readconformPDB decoys/T0139.try3-opt.pdb // NameConform T0139.try26-try3 // readconformPDB decoys/T0139.try14-opt.pdb // NameConform T0139.try26-try14 // readconformPDB decoys/T0139.try18-opt.pdb // NameConform T0139.try26-try18 // readconformPDB decoys/T0139.try19-opt.pdb // NameConform T0139.try26-try19 // readconformPDB decoys/T0139.try20-opt.pdb // NameConform T0139.try26-try20 // readconformPDB decoys/T0139.try21-opt.pdb // NameConform T0139.try26-try21 // readconformPDB decoys/T0139.try22-opt.pdb // NameConform T0139.try26-try22 // readconformPDB decoys/T0139.try23-opt.pdb // NameConform T0139.try26-try23 // readconformPDB decoys/T0139.try24-opt.pdb // NameConform T0139.try26-try24 // readconformPDB decoys/T0139.try25-opt.pdb // NameConform T0139.try26-try25 // readconformPDB decoys/T0139.try3-opt.pdb // NameConform T0139.try27-try3 // readconformPDB decoys/T0139.try14-opt.pdb // NameConform T0139.try27-try14 // readconformPDB decoys/T0139.try18-opt.pdb // NameConform T0139.try27-try18 // readconformPDB decoys/T0139.try19-opt.pdb // NameConform T0139.try27-try19 // readconformPDB decoys/T0139.try20-opt.pdb // NameConform T0139.try27-try20 // readconformPDB decoys/T0139.try21-opt.pdb // NameConform T0139.try27-try21 // readconformPDB decoys/T0139.try22-opt.pdb // NameConform T0139.try27-try22 // readconformPDB decoys/T0139.try23-opt.pdb // NameConform T0139.try27-try23 // readconformPDB decoys/T0139.try24-opt.pdb // NameConform T0139.try27-try24 // readconformPDB decoys/T0139.try25-opt.pdb // NameConform T0139.try27-try25 // readconformPDB decoys/T0139.try26.5.20.pdb // NameConform T0139.try27-try26-5 // readconformPDB decoys/T0139.try21-opt.pdb // NameConform T0139.try28-try21 // readconformPDB decoys/T0139-moved.pdb // NameConform T0139.try29 //readconformPDB decoys/T0139-moved.pdb // NameConform T0139.try30 // readconformPDB decoys/T0139.try30-opt.pdb // NameConform T0139.try31-try30 // readconformPDB decoys/T0139.try31-opt.pdb // NameConform T0139.try32-try31 // readconformPDB decoys/T0139.try32.9.40.pdb // NameConform T0139.try33-try32-9 // readconformPDB decoys/T0139.try32.1.40.pdb // NameConform T0139.try33-try32-1 // readconformPDB decoys/T0139.try32.7.40.pdb // NameConform T0139.try33-try32-7 // readconformPDB decoys/T0139.try32.8.40.pdb // NameConform T0139.try33-try32-8 // readconformPDB decoys/T0139.try32.2.40.pdb // NameConform T0139.try33-try32-2 // readconformPDB decoys/T0139.try32.6.40.pdb // NameConform T0139.try33-try32-6 // readconformPDB decoys/T0139.try32.3.40.pdb // NameConform T0139.try33-try32-3 // readconformPDB decoys/T0139.try32.4.40.pdb // NameConform T0139.try33-try32-4 // readconformPDB decoys/T0139.try31-opt.pdb // NameConform T0139.try33-try31 // readconformPDB decoys/T0139.try32-opt.pdb // NameConform T0139.try33-try32 // readconformPDB decoys/T0139.try32-opt-scwrl.pdb // NameConform T0139.try33-try32-s readconformPDB decoys/T0139.try33-opt-scwrl.pdb NameConform T0139.try34-try33-s readconformPDB decoys/T0139.try33-opt.pdb NameConform T0139.try34-try33 readconformPDB decoys/T0139.try33-try32-9.9.40.pdb NameConform T0139.try34-try33-9 ReportCost undertaker-try34.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative //NameConform T0139.try34-al2 //PrintConformPDB T0139.try34-al2.pdb edges //TryAllAlign shrink 0. min_keep_length 1 //TryAllAlign shrink 0. min_keep_length 1 cumulative //NameConform T0139.try34-al4 //PrintConformPDB T0139.try34-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative //NameConform T0139.try34-al6 //PrintConformPDB T0139.try34-al6.pdb edges //TryAllAlign shrink 0.1 min_keep_length 2 //TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0139.try34-al8 // PrintConformPDB T0139.try34-al8.pdb edges //TryAllAlign shrink 0.2 min_keep_length 3 //TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0139.try34-al10 // PrintConformPDB T0139.try34-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0139.try34-al12 // PrintConformPDB T0139.try34-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 T0139.t2k.frag OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0.5 \ ClashingRotamer 1 \ InsertFragment 1 \ CrossOver 0 \ CrossAndInsert 0.5 \ TwoFragment 1 \ InsertSpecificFragment 2 \ CloseGap 0.1 \ JiggleSubtree 0.07 \ OptSubtree 0.07 \ ReduceBreak 1 \ ReduceClash 1 \ ReduceConstraint 2 \ InsertSSBond 0 NameConform T0139.try34 OptConform pool_size 70 num_gen 30 gen_size 180 super_iter 7 \ scwrl_each use_all pdb NameConform T0139.try34-opt PrintConformPDB T0139.try34-opt.pdb edges SCWRLConform NameConform T0139.try34-opt-scwrl PrintConformPDB T0139.try34-opt-scwrl.pdb CostConform Time quit