// To be run from pce/casp5/t0159 SetSeed 1027873614 InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0159.rand Time InFilePrefix Include T0159.t2k.undertaker-align.script ReadFragmentAlignment T0159.t2k-2track-undertaker.a2m InFilePrefix 1ii5A/ Include read-alignments.under InFilePrefix 1wdnA/ Include read-alignments.under InFilePrefix 1gggB/ Include read-alignments.under InFilePrefix 1sbp/ Include read-alignments.under InFilePrefix 1ftkA/ Include read-alignments.under InFilePrefix 1gr2A/ Include read-alignments.under InFilePrefix 1iiwA/ Include read-alignments.under InFilePrefix 1wod/ Include read-alignments.under InFilePrefix 1amf/ Include read-alignments.under InFilePrefix 1lst/ Include read-alignments.under InFilePrefix 1ccwA/ Include read-alignments.under InFilePrefix 1e5dA/ Include read-alignments.under InFilePrefix 1kgsA/ Include read-alignments.under InFilePrefix 1e6mA/ Include read-alignments.under InFilePrefix 1cl1A/ Include read-alignments.under InFilePrefix 1cl2A/ Include read-alignments.under InfilePrefix Time ReportCost undertaker-try1.rdb TryAllAlign shrink 0.4 min_keep_length 5 TryAllAlign shrink 0.4 min_keep_length 5 cumulative NameConform T0159.try1-al2 PrintConformPDB T0159.try1-al2.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0159.try1-al4 PrintConformPDB T0159.try1-al4.pdb edges TryAllAlign shrink 0.3 min_keep_length 4 TryAllAlign shrink 0.3 min_keep_length 4 cumulative NameConform T0159.try1-al6 PrintConformPDB T0159.try1-al6.pdb edges TryAllAlign shrink 0.1 min_keep_length 2 TryAllAlign shrink 0.1 min_keep_length 2 cumulative NameConform T0159.try1-al8 PrintConformPDB T0159.try1-al8.pdb edges TryAllAlign shrink 0.2 min_keep_length 3 TryAllAlign shrink 0.2 min_keep_length 3 cumulative NameConform T0159.try1-al10 PrintConformPDB T0159.try1-al10.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0159.try1-al12 PrintConformPDB T0159.try1-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 T0159.t2k.frag InFilePrefix Time InitMethodProbs InsertAlignment 0.3 \ ClashingRotamer 0.5 \ InsertFragment 1 \ CrossAndInsert 1 \ TwoFragment 1 \ InsertSpecificFragment 1.5 \ ReduceBreak 5 \ CloseGap 0.01 \ ReduceClash 1 \ InsertSSBond 0 NameConform T0159.try1 OptConform pool_size 40 num_gen 20 gen_size 120 super_iter 20 pdb scwrl_each NameConform T0159.try1-opt PrintConformPDB T0159.try1-opt.pdb edges CostConform Time quit