// To be run from pce/casp5/t0158 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0158.rand Time InFilePrefix ReadTemplateAtoms Template.Atoms Include T0158.t2k.undertaker-align.script ReadFragmentAlignment T0158.t2k-2track-undertaker.a2m InFilePrefix 1jjiA/ Include read-alignments.under InFilePrefix 1jkmA/ Include read-alignments.under InFilePrefix 1jkmB/ Include read-alignments.under InFilePrefix 1evqA/ Include read-alignments.under InFilePrefix 1qe3A/ Include read-alignments.under InFilePrefix 1qidA/ Include read-alignments.under InFilePrefix 1vxrA/ Include read-alignments.under InFilePrefix 1ea5A/ Include read-alignments.under InFilePrefix 1thg/ Include read-alignments.under InFilePrefix 2bce/ Include read-alignments.under InFilePrefix 1c2oA/ Include read-alignments.under InFilePrefix 1c2bA/ Include read-alignments.under InFilePrefix 1mahA/ Include read-alignments.under InFilePrefix 1maaD/ Include read-alignments.under InFilePrefix 1fj2A/ Include read-alignments.under InFilePrefix 1jjfA/ Include read-alignments.under InFilePrefix 1auoA/ Include read-alignments.under InFilePrefix 1brt/ Include read-alignments.under InFilePrefix 1din/ Include read-alignments.under InFilePrefix 1qfmA/ Include read-alignments.under InFilePrefix InFilePrefix decoys/ // ReadConformPDB T0158.try3-opt-scwrl.pdb // NameConform T0158.try4-try3-scwrl // ReadConformPDB T0158.try1-opt.pdb // NameConform T0158.try4-try1 // ReadConformPDB T0158.try1-opt-scwrl.pdb // NameConform T0158.try5-try1-scwrl // ReadConformPDB T0158.try5-opt.pdb // NameConform T0158.try6-try5-scwrl ReadConformPDB T0158.try7-opt.pdb NameConform T0158.try8-try7-scwrl InFilePrefix Time ReportCost undertaker-try8.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0158.try8-al2 // PrintConformPDB T0158.try8-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0158.try8-al4 // PrintConformPDB T0158.try8-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0158.try8-al6 // PrintConformPDB T0158.try8-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0158.try8-al8 // PrintConformPDB T0158.try8-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0158.try8-al10 // PrintConformPDB T0158.try8-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0158.try8-al12 // PrintConformPDB T0158.try8-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 T0158.t2k.frag InFilePrefix 1jkmA/ Include read-alignments.under InFilePrefix 1jkmB/ Include read-alignments.under InFilePrefix 1evqA/ Include read-alignments.under InFilePrefix 1qe3A/ Include read-alignments.under InFilePrefix 1qidA/ Include read-alignments.under InFilePrefix 1vxrA/ Include read-alignments.under InFilePrefix 1ea5A/ Include read-alignments.under InFilePrefix 1thg/ Include read-alignments.under InFilePrefix 2bce/ Include read-alignments.under InFilePrefix 1c2oA/ Include read-alignments.under InFilePrefix 1c2bA/ Include read-alignments.under InFilePrefix 1mahA/ Include read-alignments.under InFilePrefix 1maaD/ Include read-alignments.under InFilePrefix 1fj2A/ Include read-alignments.under InFilePrefix 1jjfA/ Include read-alignments.under InFilePrefix 1auoA/ Include read-alignments.under InFilePrefix 1brt/ Include read-alignments.under InFilePrefix 1din/ Include read-alignments.under InFilePrefix 1qfmA/ Include read-alignments.under InFilePrefix OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0.1 \ ClashingRotamer 2 \ InsertFragment 5 \ CrossAndInsert 1 \ TwoFragment 3 \ InsertSpecificFragment 5 \ ReduceBreak 1 \ CloseGap 0.2 \ OptSubtree 0.03 \ JiggleSubtree 0.03 \ ReduceClash 1 \ InsertSSBond 0 \ ImproveSSBond 1 NameConform T0158.try8 OptConform pool_size 40 num_gen 50 gen_size 180 super_iter 7 \ pdb use_all scwrl_each NameConform T0158.try8-opt PrintConformPDB T0158.try8-opt.pdb edges SCWRLConform NameConform T0158.try8-opt-scwrl PrintConformPDB T0158.try8-opt-scwrl.pdb CostConform Time quit