// To be run from pce/casp5/t0137 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0137.rand Time // The following alignments are believed to be good: InFilePrefix ReadTemplateAtoms Template.atoms Include T0137.undertaker-align.script ReadFragmentAlignment T0137.t2k-2track-undertaker.a2m InFilePrefix 1crb/ include read-alignments.under InFilePrefix 1hmt/ include read-alignments.under InFilePrefix 1hms/ include read-alignments.under InFilePrefix 1lid/ include read-alignments.under InFilePrefix 1bwyA/ include read-alignments.under InFilePrefix 1opbA/ include read-alignments.under InFilePrefix 1opaA/ include read-alignments.under InFilePrefix 1cbs/ include read-alignments.under InFilePrefix 1ifc/ include read-alignments.under InFilePrefix 1ftpA/ include read-alignments.under InFilePrefix 1fdqA/ include read-alignments.under InFilePrefix 1a2dA/ include read-alignments.under InFilePrefix 1pmpA/ include read-alignments.under InFilePrefix 1ab0/ include read-alignments.under InFilePrefix 1acd/ include read-alignments.under InFilePrefix 1jjjA/ include read-alignments.under InFilePrefix Time ReadConformPDB decoys/T0137.try4-opt-scwrl.pdb NameConform T0137.try5-try4 ReportCost undertaker-try5.rdb TryAllAlign shrink 0.4 min_keep_length 5 TryAllAlign shrink 0.4 min_keep_length 5 cumulative NameConform T0137.try5-al2 PrintConformPDB T0137.try5-al2.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0137.try5-al4 PrintConformPDB T0137.try5-al4.pdb edges TryAllAlign shrink 0.3 min_keep_length 4 TryAllAlign shrink 0.3 min_keep_length 4 cumulative NameConform T0137.try5-al6 PrintConformPDB T0137.try5-al6.pdb edges TryAllAlign shrink 0.1 min_keep_length 2 TryAllAlign shrink 0.1 min_keep_length 2 cumulative NameConform T0137.try5-al8 PrintConformPDB T0137.try5-al8.pdb edges TryAllAlign shrink 0.2 min_keep_length 3 TryAllAlign shrink 0.2 min_keep_length 3 cumulative NameConform T0137.try5-al10 PrintConformPDB T0137.try5-al10.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0137.try5-al12 PrintConformPDB T0137.try5-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 T0137.t2k.frag OutFilePrefix printTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0 \ ClashingRotamer 0.5 \ InsertFragment 3 \ CrossAndInsert 1 \ TwoFragment 1 \ InsertSpecificFragment 3 \ ReduceBreak 1 \ CloseGap 0.1 \ OptSubtree 0.03 \ JiggleSubtree 0.04 \ ReduceClash 1 \ InsertSSBond 0 NameConform T0137.try5 OptConform pool_size 40 num_gen 60 gen_size 180 super_iter 20 \ scwrl_each use_all pdb NameConform T0137.try5-opt PrintConformPDB T0137.try5-opt.pdb edges ScwrlConform NameConform T0137.try5-opt-scwrl PrintConformPDB T0137.try5-opt-scwrl.pdb CostConform Time quit