// To be run from pce/casp5/t0138 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0138.rand Time InFilePrefix ReadTemplateAtoms Template.atoms // The following alignments are believed to be good: InFilePrefix Include T0138.undertaker-align.script ReadFragmentAlignment T0138.t2k-2track-undertaker.a2m InFilePrefix 1dbwA/ Include read-alignments.under InFilePrefix 1dckA/ Include read-alignments.under InFilePrefix 1jjfA/ Include read-alignments.under InFilePrefix 1bouB/ Include read-alignments.under InFilePrefix 1d5wC/ Include read-alignments.under InFilePrefix 1kgsA/ Include read-alignments.under InFilePrefix 1ntr/ Include read-alignments.under InFilePrefix // The next few alignments come from structural alignments of // decoys/T0138-try14-opt-scwrl done by VAST. ReadFragmentAlignment T0138-2minB.vast ReadFragmentAlignment T0138-1dcfA.vast ReadFragmentAlignment T0138-1jkmB.vast ReadFragmentAlignment T0138-1ac5.vast ReadFragmentAlignment T0138-1jv2B.vast ReadFragmentAlignment T0138-1scuA.vast ReadFragmentAlignment T0138-3chy.vast ReadFragmentAlignment T0138-1ejbA.vast Time // ReadConformPDB decoys/T0138.try10-opt-scwrl.pdb // NameConform T0138.try14-try10 // ReadConformPDB decoys/T0138.try8-opt-scwrl.pdb // NameConform T0138.try14-try8 // ReadConformPDB decoys/T0138.try6-opt-scwrl.pdb // NameConform T0138.try14-try6 // ReadConformPDB decoys/T0138.try4-opt.pdb // NameConform T0138.try14-try4 // ReadConformPDB decoys/T0138.try7-opt-scwrl.pdb // NameConform T0138.try14-try7 // ReadConformPDB decoys/T0138.try4+1bouB-T0138-vit-adp...+T0138-1dckA-2track-protein-EBGHTL-global-adpstyle5.pw.a2m.gz:1dckA.12.20.pdb // NameConform T0138.try9-try4...1dckA // ReadConformPDB decoys/T0138.try11-opt-scwrl.pdb // NameConform T0138.try12-try11 // ReadConformPDB decoys/T0138.try12-opt-scwrl.pdb // NameConform T0138.try13-try12 // ReadConformPDB decoys/T0138.try13-opt.pdb // NameConform T0138.try14-try13 // ReadConformPDB decoys/T0138.try14-opt-scwrl.pdb // NameConform T0138.try16-try14 // ReadConformPDB decoys/T0138.try15-opt-scwrl.pdb // NameConform T0138.try16-try15 InFilePrefix decoys/T0138. // read in the lowest scores from each of the runs 12,13,15,16,17 // ReadConformPDB try12.25.30.pdb // NameConform T0138.try18-try12-25 // ReadConformPDB try13-opt.pdb // NameConform T0128.try18-try13 // ReadConformPDB try15-opt-scwrl.pdb // NameConform T0128.try18-try15 // ReadConformPDB try16.15.40.pdb // NameConform T0128.try18-try16-15 // ReadConformPDB try17-opt.pdb // NameConform T0128.try18-try17 // read in the lowest-cost decoys with the current try18 scoring function // ReadConformPDB try14.24.30.pdb // NameConform T0138.try18-try14-24 // ReadConformPDB try14.14.30.pdb // NameConform T0138.try18-try14-14 // ReadConformPDB try14.21.30.pdb // NameConform T0138.try18-try14-21 // This was the best previous scorer. // ReadConformPDB try14.9.30.pdb // NameConform T0138.try18-try14-9 // ReadConformPDB try18-opt.pdb // NameConform T0138.try19-try18 // ReadConformPDB try18-opt.pdb // NameConform T0138.try20-try18 // ReadConformPDB try18-opt-scwrl.pdb // NameConform T0138.try20-try19 // ReadConformPDB try8-opt.pdb // NameConform T0138.try21-try8 // ReadConformPDB try9-opt.pdb // NameConform T0138.try21-try9 // ReadConformPDB try18-opt.pdb // NameConform T0138.try21-try18 // ReadConformPDB try19-opt-scwrl.pdb // NameConform T0138.try21-try19 // ReadConformPDB try20-opt-scwrl.pdb // NameConform T0138.try21-try20 // ReadConformPDB try21-opt.pdb // NameConform T0138.try22-try21 // ReadConformPDB try22-opt.pdb // NameConform T0138.try23-try22 // ReadConformPDB try23-opt.pdb // NameConform T0138.try24-try23 // ReadConformPDB try24-opt.pdb // NameConform T0138.try25-try24 ReadConformPDB try25.14.80.pdb NameConform T0138.try26-try25-14 ReadConformPDB try25.10.80.pdb NameConform T0138.try26-try25-10 ReadConformPDB try25-opt.pdb NameConform T0138.try26-try25 ReadConformPDB try25.17.80.pdb NameConform T0138.try26-try25-17 ReadConformPDB try25.2.80.pdb NameConform T0138.try26-try25-2 InFilePrefix ReportCost undertaker-try26.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative //NameConform T0138.try26-al2 //PrintConformPDB T0138.try26-al2.pdb edges //TryAllAlign shrink 0. min_keep_length 1 //TryAllAlign shrink 0. min_keep_length 1 cumulative //NameConform T0138.try26-al4 //PrintConformPDB T0138.try26-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative //NameConform T0138.try26-al6 //PrintConformPDB T0138.try26-al6.pdb edges //TryAllAlign shrink 0.1 min_keep_length 2 //TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0138.try26-al8 // PrintConformPDB T0138.try26-al8.pdb edges //TryAllAlign shrink 0.2 min_keep_length 3 //TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0138.try26-al10 // PrintConformPDB T0138.try26-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0138.try26-al12 // PrintConformPDB T0138.try26-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. ReadFragmentAlignment T0138.t2k.frag InFilePrefix // OutFilePrefix // PrintTemplateAtoms Template.atoms // OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0.1 \ ClashingRotamer 0.5 \ InsertFragment 8 \ CrossOver 0 \ CrossAndInsert 4 \ TwoFragment 2 \ InsertSpecificFragment 3 \ ReduceBreak 1 \ CloseGap 0.5 \ ReduceClash 4 \ ImproveSSBond 0 \ ReduceConstraint 0 \ JiggleSubtree 0.02 \ OptSubtree 0.02 \ InsertSSBond 0 NameConform T0138.try26 OptConform pool_size 70 num_gen 80 gen_size 200 super_iter 20 \ pdb scwrl_each use_all NameConform T0138.try26-opt PrintConformPDB T0138.try26-opt.pdb edges SCWRLConform NameConform T0138.try26-opt-scwrl PrintConformPDB T0138.try26-opt-scwrl.pdb edges CostConform Time quit