// To be run from pce/casp5/t0133 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0133.rand Time InFilePrefix ReadTemplateAtoms Template.atoms InFilePrefix Include T0133.undertaker-align.script ReadFragmentAlignment T0133.t2k-2track-undertaker.a2m InFilePrefix 1hg5A/ Include read-alignments.under InFilePrefix 1hf8A/ Include read-alignments.under InFilePrefix 1hx8B/ Include read-alignments.under InFilePrefix 1eduA/ Include read-alignments.under InFilePrefix 1eyhA/ Include read-alignments.under InFilePrefix 1gw5A/ Include read-alignments.under InFilePrefix 1xikA/ Include read-alignments.under InFilePrefix 1jqcA/ Include read-alignments.under InFilePrefix 1ribA/ Include read-alignments.under InFilePrefix // ReadConformPDB decoys/T0133.try4-opt-scwrl.pdb // NameConform T0133.try7-try4 // ReadConformPDB decoys/T0133.try5-opt-scwrl.pdb // NameConform T0133.try7-try5 // ReadConformPDB decoys/T0133.try6-al10+1jqcA-T0133-local-adpstyle1.pw.a2m.gz:1jqcA.10.20.pdb // NameConform T0133.try7-try6 // ReadConformPDB decoys/T0133.try8-opt-scwrl.pdb // NameConform T0133.try9-try8 // ReadConformPDB decoys/T0133.try9-opt.pdb // NameConform T0133.try10-try9 // ReadConformPDB decoys/T0133.try7-opt.pdb // NameConform T0133.try11-try7 // ReadConformPDB decoys/T0133.try7-opt-scwrl.pdb // NameConform T0133.try12-try7 // ReadConformPDB decoys/T0133.try11-opt-scwrl.pdb // NameConform T0133.try12-try11-scwrl // ReadConformPDB decoys/T0133.try11-opt.pdb // NameConform T0133.try12-try11 // ReadConformPDB decoys/T0133.try11-opt.pdb // NameConform T0133.try14-try11 // ReadConformPDB decoys/T0133.try12-opt.pdb // NameConform T0133.try14-try12 // ReadConformPDB decoys/T0133.try13-opt-scwrl.pdb // NameConform T0133.try14-try13 ReadConformPDB decoys/T0133.try14-opt-scwrl.pdb NameConform T0133.try15-try14 Time ReportCost undertaker-try15.rdb TryAllAlign shrink 0.4 min_keep_length 5 TryAllAlign shrink 0.4 min_keep_length 5 cumulative NameConform T0133-try15.al2 PrintConformPDB T0133-try15.al2.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0133.try15-al4 PrintConformPDB T0133.try15-al4.pdb edges TryAllAlign shrink 0.3 min_keep_length 4 TryAllAlign shrink 0.3 min_keep_length 4 cumulative NameConform T0133.try15-al6 PrintConformPDB T0133.try15-al6.pdb edges TryAllAlign shrink 0.1 min_keep_length 2 TryAllAlign shrink 0.1 min_keep_length 2 cumulative NameConform T0133.try15-al8 PrintConformPDB T0133.try15-al8.pdb edges TryAllAlign shrink 0.2 min_keep_length 3 TryAllAlign shrink 0.2 min_keep_length 3 cumulative NameConform T0133.try15-al10 PrintConformPDB T0133.try15-al10.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0133.try15-al12 PrintConformPDB T0133.try15-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 T0133.t2k.frag InFilePrefix OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0.01 \ ClashingRotamer 0.5 \ InsertFragment 5 \ CrossOver 0 \ CrossAndInsert 3 \ TwoFragment 1 \ InsertSpecificFragment 4 \ ReduceBreak 1 \ CloseGap 0.3 \ OptSubtree 0.03 \ JiggleSubtree 0.02 \ ReduceClash 1 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0133.try15 OptConform pool_size 50 num_gen 60 gen_size 150 super_iter 20 \ pdb use_all scwrl_each NameConform T0133.try15-opt PrintConformPDB T0133.try15-opt.pdb edges SCWRLConform NameConform T0133.try15-opt-scwrl PrintConformPDB T0133.try15-opt-scwrl.pdb CostConform Time quit