// To be run from pce/casp5/t0179 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0179.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0179.t2k.undertaker-align.script ReadFragmentAlignment T0179.t2k-2track-undertaker.a2m InfilePrefix 1inlA/ include read-alignments.under InfilePrefix 1jq3A/ include read-alignments.under InfilePrefix 1i1nA/ include read-alignments.under InfilePrefix 1dusA/ include read-alignments.under InfilePrefix 1kr5A/ include read-alignments.under InfilePrefix 1xvaA/ include read-alignments.under InfilePrefix 1im8A/ include read-alignments.under InfilePrefix Time ReadConformPDB decoys/T0179.try1-opt-scwrl.pdb NameConform T0179.try2-try1 ReportCost undertaker-try2.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0179.try2-al2 // PrintConformPDB T0179.try2-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0179.try2-al4 // PrintConformPDB T0179.try2-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0179.try2-al6 // PrintConformPDB T0179.try2-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0179.try2-al8 // PrintConformPDB T0179.try2-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0179.try2-al10 // PrintConformPDB T0179.try2-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0179.try2-al12 // PrintConformPDB T0179.try2-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 T0179.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 0.1 \ InsertFragment 10 \ CrossAndInsert 1 \ CrossOver 0 \ TwoFragment 1 \ InsertSpecificFragment 5 \ ReduceBreak 5 \ CloseGap 0.1 \ ReduceClash 1 \ JiggleSubtree 0.04 \ OptSubtree 0.04 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0179.try2 OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 10 pdb NameConform T0179.try2-opt PrintConformPDB T0179.try2-opt.pdb edges SCWRLConform NameConform T0179.try2-opt-scwrl PrintConformPDB T0179.try2-opt-scwrl.pdb CostConform Time quit