// To be run from pce/casp5/t0141 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time // The following alignments are believed to be good: InFilePrefix InFilePrefix Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms InFilePrefix Include T0141.undertaker-align.script ReadFragmentAlignment T0141.t2k-2track-undertaker.a2m InFilePrefix 1aroL/ include read-alignments.under InFilePrefix 1lba/ include read-alignments.under InFilePrefix Time // ReadConformPDB decoys/T0141.try6-opt-scwrl.pdb // NameConform T0141.try7-try6 // ReadConformPDB decoys/T0141.try6-opt-scwrl.pdb // NameConform T0141.try8-try6 // ReadConformPDB decoys/T0141.try7-opt-scwrl.pdb // NameConform T0141.try8-try7 // ReadConformPDB decoys/T0141.try8-opt.pdb // NameConform T0141.try9-try8 // ReadConformPDB decoys/T0141-moved.pdb // NameConform T0141.try10-moved // ReadConformPDB decoys/T0141.try10-opt-scwrl.pdb // NameConform T0141.try11-try10 // ReadConformPDB decoys/T0141.try11-opt.pdb // NameConform T0141.try12-try11 // ReadConformPDB decoys/T0141-moved2.pdb // NameConform T0141.try13 // ReadConformPDB decoys/T0141.cut-and-paste.pdb // NameConform T0141.try14 // ReadConformPDB decoys/T0141.try14-opt.pdb // NameConform T0141.try15-try14 // ReadConformPDB decoys/T0141.try14-opt.pdb // NameConform T0141.try16-try14 // ReadConformPDB decoys/T0141.try15-opt-scwrl.pdb // NameConform T0141.try16-try15-s // ReadConformPDB decoys/T0141.try15.9.90.pdb // NameConform T0141.try16-try15-9 // ReadConformPDB decoys/T0141.try15.8.90.pdb // NameConform T0141.try16-try15-8 // ReadConformPDB decoys/T0141.try15.9.90.pdb // NameConform T0141.try16-try15-9 // ReadConformPDB decoys/T0141.try16-opt.pdb // NameConform T0141.try17-try16 // ReadConformPDB decoys/T0141.try16-opt-scwrl.pdb // NameConform T0141.try17-try16-s // ReadConformPDB decoys/T0141.try16-scwrl.10.100.pdb // NameConform T0141.try17-try16-10 // ReadConformPDB decoys/T0141.try16.2.100.pdb // NameConform T0141.try17-try16-2 // ReadConformPDB decoys/T0141.try17-opt-scwrl.pdb // NameConform T0141.try18-try17-s // ReadConformPDB decoys/T0141.try17.1.50.pdb // NameConform T0141.try18-try17-1 // ReadConformPDB decoys/T0141.try17.4.50.pdb // NameConform T0141.try18-try17-4 // ReadConformPDB decoys/T0141.try17.3.50.pdb // NameConform T0141.try18-try17-3 // ReadConformPDB decoys/T0141.try17.5.50.pdb // NameConform T0141.try18-try17-5 // ReadConformPDB decoys/T0141.try17.2.50.pdb // NameConform T0141.try18-try17-2 // ReadConformPDB decoys/T0141.try15.9.90.pdb // NameConform T0141.try19-try15-9 // ReadConformPDB decoys/T0141.try18.1.50.pdb // NameConform T0141.try19-try18-1 // ReadConformPDB decoys/T0141.try16.7.100.pdb // NameConform T0141.try19-try16-7 // ReadConformPDB decoys/T0141.try18.3.50.pdb // NameConform T0141.try19-try18-3 // ReadConformPDB decoys/T0141.try18.3.50.pdb // NameConform T0141.try19-try18-3 // ReadConformPDB decoys/T0141.try17-opt-scwrl.pdb // NameConform T0141.try19-try17-s ReadConformPDB decoys/T0141.try17-opt-scwrl.pdb NameConform T0141.try20-try17-s ReadConformPDB decoys/T0141.try18.3.50.pdb NameConform T0141/try20-try18-3 ReadConformPDB decoys/T0141.try19-opt-scwrl.pdb NameConform T0141/try20-try19-s ReadConformPDB decoys/T0141.try19-try16-7.1.50.pdb NameConform T0141/try20-try19-1 ReadConformPDB decoys/T0141.try19-try16-7.5.50.pdb NameConform T0141/try20-try19-5 ReportCost undertaker-try20.rdb // ConformFromSeq replace // get a random conformation, removing all-zero one // NameConform T0141.rand // Time // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0141.try20-al2 // PrintConformPDB T0141.try20-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0141.try20-al4 // PrintConformPDB T0141.try20-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0141.try20-al6 // PrintConformPDB T0141.try20-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0141.try20-al8 // PrintConformPDB T0141.try20-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0141.try20-al10 // PrintConformPDB T0141.try20-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0141.try20-al12 // PrintConformPDB T0141.try20-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 T0141.t2k.frag OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0 \ ClashingRotamer 4 \ InsertFragment 20 \ CrossAndInsert 1 \ CrossOver 0 \ TwoFragment 1 \ InsertSpecificFragment 5 \ ReduceBreak 1 \ CloseGap 0.2 \ OptSubtree 0.03 \ JiggleSubtree 0.03 \ Reduceclash 2 \ InsertSSBond 0 NameConform T0141.try20 OptConform pool_size 40 num_gen 100 gen_size 200 super_iter 10 pdb \ use_all scwrl_each NameConform T0141.try20-opt PrintConformPDB T0141.try20-opt.pdb edges SCWRLConform NameConform T0141.try20-opt-scwrl PrintConformPDB T0141.try20-opt-scwrl.pdb edges CostConform Time quit