// To be run from pce/casp5/t0147 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateatoms Template.atoms Time // ReadConformPDB robetta1.pdb // nameConform T0147.try3-robetta1 // ReadConformPDB decoys/T0147.try2-opt-scwrl.pdb // nameConform T0147.try7-try2 // ReadConformPDB decoys/T0147.try3-opt-scwrl.pdb // nameConform T0147.try7-try3 // ReadConformPDB decoys/T0147.try3-robetta1.16.60.pdb // nameConform T0147.try9-try3-16 // ReadConformPDB decoys/T0147.try4-opt.pdb // nameConform T0147.try9-try4 // ReadConformPDB decoys/T0147.try5.7.60.pdb // nameConform T0147.try9-try5-7 // ReadConformPDB decoys/T0147.try6-opt-scwrl.pdb // nameConform T0147.try9-try6 // ReadConformPDB decoys/T0147.try7.13.40.pdb // nameConform T0147.try9-try7-13 // ReadConformPDB decoys/T0147.try6-opt-scwrl.pdb // NameConform T0147.try13-try6 // ReadConformPDB decoys/T0147.try9-opt-scwrl.pdb // NameConform T0147.try13-try9 // ReadConformPDB decoys/T0147.try10-opt.pdb // NameConform T0147.try13-try10 // ReadConformPDB decoys/T0147.try11-opt.pdb // NameConform T0147.try13-try11 // ReadConformPDB decoys/T0147.try6-opt-scwrl.pdb // NameConform T0147.try14-try6 // ReadConformPDB decoys/T0147.try9-opt-scwrl.pdb // NameConform T0147.try14-try9 // ReadConformPDB decoys/T0147.try10-opt.pdb // NameConform T0147.try14-try10 // ReadConformPDB decoys/T0147.try11-opt.pdb // NameConform T0147.try14-try11 // ReadConformPdb decoys/T0147.try12-opt-scwrl.pdb // NameConform T0147.try14-try12 // ReadConformPdb decoys/T0147.try13-opt-scwrl.pdb // NameConform T0147.try14-try13 // ReadConformPDB decoys/T0147-moved14.pdb // NameConform T0147.try15-moved // ReadConformPDB decoys/T0147.try15-opt-scwrl.pdb // NameConform T0147.try16-try15 // ReadConformPDB decoys/T0147-moved16.pdb // NameConform T0147.try17-moved // ReadConformPDB decoys/T0147.try11-opt-scwrl.pdb // NameConform T0147.try18-try11 // ReadConformPDB decoys/T0147.try12-al10.5.60.pdb // NameConform T0147.try18-try12-5 // ReadConformPDB decoys/T0147.try16-opt.pdb // NameConform T0147.try18-try16 // ReadConformPDB decoys/T0147.try13-opt.pdb // NameConform T0147.try18-try13 // ReadConformPDB decoys/T0147.try14-opt.pdb // NameConform T0147.try18-try14 // ReadConformPDB decoys/T0147.try15.2.40.pdb // NameConform T0147.try18-try15-2 // ReadConformPDB decoys/T0147.try17-opt-scwrl.pdb // NameConform T0147.try18-try17 // ReadConformPDB decoys/T0147.try11-opt-scwrl.pdb // NameConform T0147.try19-try11 // ReadConformPDB decoys/T0147.try12-opt-scwrl.pdb // NameConform T0147.try19-try12 // ReadConformPDB decoys/T0147.try16-opt.pdb // NameConform T0147.try19-try16 // ReadConformPDB decoys/T0147.try13-try11.5.60.pdb // NameConform T0147.try19-try13-5 // ReadConformPDB decoys/T0147.try14-opt.pdb // NameConform T0147.try19-try14 // ReadConformPDB decoys/T0147.try15.2.40.pdb // NameConform T0147.try19-try15-2 // ReadConformPDB decoys/T0147.try17-opt-scwrl.pdb // NameConform T0147.try19-try17 // ReadConformPDB decoys/T0147.try18-opt-scwrl.pdb // NameConform T0147.try19-try18 // ReadConformPDB decoys/T0147.try16-opt.pdb // NameConform T0147.try20-try16 // ReadConformPDB decoys/T0147.try15.2.40.pdb // NameConform T0147.try20-try15-2 // ReadConformPDB decoys/T0147.try17-opt-scwrl.pdb // NameConform T0147.try20-try17 // ReadConformPDB decoys/T0147.try18-opt.pdb // NameConform T0147.try20-try18 // ReadConformPDB decoys/T0147.try19-opt-scwrl.pdb // NameConform T0147.try20-try19 ReadConformPDB decoys/T0147.try9-try6.4.80.pdb NameConform T0147.try21-try9-4 ReportCost undertaker-try21.rdb // ConformFromSeq replace // pop all zeros // ConformFromSeq // don't pop good conformation!n // NameConform T0147.rand Time ReadfragmentAlignment 1ezwA/T0147-1ezwA-hand.a2m // TryAllAlign TryAllAlign shrink 0. min_keep_length 1 // NameConform T0147.try9-1ezwA Include T0147.t2k.undertaker-align.script ReadFragmentAlignment T0147.t2k-2track-undertaker.a2m InFilePrefix 1fwcC/ include read-alignments.under InFilePrefix 1ejrC/ include read-alignments.under InFilePrefix 1ubpC/ include read-alignments.under InFilePrefix 1frb/ include read-alignments.under InFilePrefix 1ezwA/ include read-alignments.under InFilePrefix 1a4mA/ include read-alignments.under InFilePrefix 1gox/ include read-alignments.under InFilePrefix 2mnr/ include read-alignments.under InFilePrefix 1mdl/ include read-alignments.under InFilePrefix // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0147.try21-al2 // PrintConformPDB T0147.try21-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0147.try21-al4 // PrintConformPDB T0147.try21-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0147.try21-al6 // PrintConformPDB T0147.try21-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0147.try21-al8 // PrintConformPDB T0147.try21-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0147.try21-al10 // PrintConformPDB T0147.try21-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0147.try21-al12 // PrintConformPDB T0147.try21-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 T0147.t2k.frag InFilePrefix OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0 \ ClashingRotamer 0.5 \ OneRotamer 0.01 \ InsertFragment 5 \ CrossAndInsert 2 \ CrossOver 0 \ TwoFragment 10 \ InsertSpecificFragment 2 \ ReduceBreak 0 \ ReduceConstraint 1 \ CloseGap 0.2 \ OptSubtree 0.03 \ JiggleSubtree 0.03 \ ReduceClash 1 \ ImproveSSBond 0 \ InsertSSBond 0 NameConform T0147.try21 OptConform pool_size 40 num_gen 80 gen_size 130 super_iter 1 \ pdb use_all // no_initial_fill // scwrl_each NameConform T0147.try21-opt PrintConformPDB T0147.try21-opt.pdb edges SCWRLconform NameConform T0147.try21-opt-scwrl PrintConformPDB T0147.try21-opt-scwrl.pdb CostConform Time quit