// To be run from pce/casp5/t0194 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0194.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0194.t2k.undertaker-align.script ReadFragmentAlignment T0194.t2k-2track-undertaker.a2m InFilePrefix 1bdg/ include read-alignments.under InFilePrefix 1opy/ include read-alignments.under InFilePrefix 1heuA/ include read-alignments.under InFilePrefix 1ee2A/ include read-alignments.under InFilePrefix 1hetA/ include read-alignments.under InFilePrefix 1qi6A/ include read-alignments.under InFilePrefix 1euhA/ include read-alignments.under InFilePrefix 1xze/ include read-alignments.under InFilePrefix 1d2nA/ include read-alignments.under InFilePrefix 9gacA/ include read-alignments.under InFilePrefix 2pgd/ include read-alignments.under InFilePrefix 1e32A/ include read-alignments.under InFilePrefix 1g6oA/ include read-alignments.under InFilePrefix 1jbkA/ include read-alignments.under InFilePrefix 1d2mA/ include read-alignments.under InfilePrefix // ReadConformPDB decoys/T0194.try2-opt-scwrl.pdb // NameConform T0194.try6-try2 // ReadConformPDB decoys/T0194.try3-opt-scwrl.pdb // NameConform T0194.try6-try3 // ReadConformPDB decoys/T0194.try5-opt-scwrl.pdb // NameConform T0194.try6-try3 // ReadConformPDB decoys/T0194.try5-opt-scwrl.pdb // NameConform T0194.try8-try5 // ReadConformPDB decoys/T0194.try6.0.60.pdb // NameConform T0194.try8-try6-0 // ReadConformPDB decoys/T0194.try6.1.60.pdb // NameConform T0194.try8-try6-1 // ReadConformPDB decoys/T0194.try5-opt-scwrl.pdb // NameConform T0194.try9-try5 // ReadConformPDB decoys/T0194.try6.0.60.pdb // NameConform T0194.try9-try6-0 // ReadConformPDB decoys/T0194.try6.1.60.pdb // NameConform T0194.try9-try6-1 // ReadConformPDB decoys/T0194.try2-opt-scwrl.pdb // NameConform T0194.try11-try2 // ReadConformPDB decoys/T0194.try4.17.60.pdb // NameConform T0194.try11-try4-17 // ReadConformPDB decoys/T0194.try2.4.60.pdb // NameConform T0194.try11-try2-4 // ReadConformPDB decoys/T0194.try4.0.60.pdb // NameConform T0194.try11-try4-0 // ReadConformPDB decoys/T0194.try3.18.60.pdb // NameConform T0194.try11-try3-18 // ReadConformPDB decoys/T0194.try9-opt.pdb // NameConform T0194.try11-try9 // ReadConformPDB decoys/T0194.try9-opt.pdb // NameConform T0194.try14-try9 // ReadConformPDB decoys/T0194.try7.1.20.pdb // NameConform T0194.try14-try7-1 // ReadConformPDB decoys/T0194.try5.15.60.pdb // NameConform T0194.try14-try5-15 // ReadConformPDB decoys/T0194.try5.10.60.pdb // NameConform T0194.try14-try5-10 // ReadConformPDB decoys/T0194.try11-opt.pdb // NameConform T0194.try14-try11 ReadConformPDB decoys/T0194.try2.4.60.pdb NameConform T0194.try15-try2-4 ReadConformPDB decoys/T0194.try9-opt.pdb NameConform T0194.try15-try9 ReadConformPDB decoys/T0194.try13.0.100.pdb NameConform T0194.try15-try13-0 ReadConformPDB decoys/T0194.try14-opt.pdb NameConform T0194.try15-try14 ReadConformPDB decoys/T0194.try11-opt.pdb NameConform T0194.try15-try11 Time ReportCost undertaker-try15.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0194.try15-al2 // PrintConformPDB T0194.try15-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0194.try15-al4 // PrintConformPDB T0194.try15-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0194.try15-al6 // PrintConformPDB T0194.try15-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0194.try15-al8 // PrintConformPDB T0194.try15-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0194.try15-al10 // PrintConformPDB T0194.try15-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0194.try15-al12 // PrintConformPDB T0194.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. InFilePrefix ReadFragmentAlignment T0194.t2k.frag // The next 3 lines save the templates in a single file, to avoid having // to reread the PDB files. Note that ReadTemplateAtoms should be called // before any ReadFragmentAlignments to take full advantage of this // cached results. OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0.3 \ ClashingRotamer 0.5 \ OneRotamer 0.02 \ InsertFragment 10 \ CrossAndInsert 10 \ CrossOver 0 \ TwoFragment 10 \ InsertSpecificFragment 10 \ ReduceBreak 5 \ CloseGap 0.1 \ ReduceClash 1 \ ReduceConstraint 1 \ JiggleSubtree 0.03 \ OptSubtree 0.03 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0194.try15 OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 1 \ use_all pdb NameConform T0194.try15-opt PrintConformPDB T0194.try15-opt.pdb edges // SCWRLConform // NameConform T0194.try15-opt-scwrl // PrintConformPDB T0194.try15-opt-scwrl.pdb CostConform Time quit