// To be run from pce/casp5/t0187 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ //ConformFromSeq replace // get a random conformation, removing all-zero one //NameConform T0187.rand //Time InFilePrefix ReadTemplateAtoms Template.atoms //Include T0187.t2k.undertaker-align.script //ReadFragmentAlignment T0187.t2k-2track-undertaker.a2m InfilePrefix Time ReadConformPDB robetta1.pdb NameConform T0174.try3-robetta1 ReadConformPDB robetta2.pdb NameConform T0174.try3-robetta2 ReportCost undertaker-try3.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0187.try3-al2 // PrintConformPDB T0187.try3-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0187.try3-al4 // PrintConformPDB T0187.try3-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0187.try3-al6 // PrintConformPDB T0187.try3-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0187.try3-al8 // PrintConformPDB T0187.try3-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0187.try3-al10 // PrintConformPDB T0187.try3-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0187.try3-al12 // PrintConformPDB T0187.try3-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 T0187.t2k.frag InfilePrefix 2pgi/ include read-alignments.under InfilePrefix 1bouB/ include read-alignments.under InfilePrefix 1gt8D/ include read-alignments.under InfilePrefix 1gthB/ include read-alignments.under InfilePrefix 1gteD/ include read-alignments.under InfilePrefix 1qopA/ include read-alignments.under InfilePrefix 1gthC/ include read-alignments.under InfilePrefix 1h7xB/ include read-alignments.under InfilePrefix 1h7wD/ include read-alignments.under InfilePrefix 1srvA/ include read-alignments.under InFilePrefix t0187-1-150/1jeoA/ include read-alignments.under InFilePrefix t0187-1-150/1bouB/ include read-alignments.under InFilePrefix t0187-1-150/1lk5A/ include read-alignments.under InFilePrefix t0187-1-150/1pdo/ include read-alignments.under InFilePrefix t0187-1-150/1bd3A/ include read-alignments.under InFilePrefix t0187-1-150/1jmyA/ include read-alignments.under InFilePrefix t0187-1-150/1f6wA/ include read-alignments.under InFilePrefix t0187-1-150/1qmgA/ include read-alignments.under InFilePrefix t0187-1-150/2pgi/ include read-alignments.under InFilePrefix t0187-1-150/1aqlA/ include read-alignments.under InFilePrefix t0187-91-240/1bouB/ include read-alignments.under InFilePrefix t0187-91-240/1xxbA/ include read-alignments.under InFilePrefix t0187-91-240/1fxkC/ include read-alignments.under InFilePrefix t0187-91-240/1dciA/ include read-alignments.under InFilePrefix t0187-91-240/1xxcA/ include read-alignments.under InFilePrefix t0187-91-240/1l2qA/ include read-alignments.under InFilePrefix t0187-91-240/1l2rA/ include read-alignments.under InFilePrefix t0187-91-240/1xxaA/ include read-alignments.under InFilePrefix t0187-91-240/1i5nA/ include read-alignments.under InFilePrefix t0187-91-240/1mroB/ include read-alignments.under InFilePrefix t0187-201-350/1srvA/ include read-alignments.under InFilePrefix t0187-201-350/1jmxA/ include read-alignments.under InFilePrefix t0187-201-350/1gajA/ include read-alignments.under InFilePrefix t0187-201-350/1g6hA/ include read-alignments.under InFilePrefix t0187-201-350/1i58A/ include read-alignments.under InFilePrefix t0187-201-350/1fukA/ include read-alignments.under InFilePrefix t0187-201-350/1akr/ include read-alignments.under InFilePrefix t0187-201-350/1ex2A/ include read-alignments.under InFilePrefix t0187-201-350/1lucA/ include read-alignments.under InFilePrefix t0187-201-350/1jztA/ include read-alignments.under InFilePrefix t0187-301-417/1je0A/ include read-alignments.under InFilePrefix t0187-301-417/1jmxA/ include read-alignments.under InFilePrefix t0187-301-417/1ex2A/ include read-alignments.under InFilePrefix t0187-301-417/1k3fA/ include read-alignments.under InFilePrefix t0187-301-417/1lx7A/ include read-alignments.under InFilePrefix t0187-301-417/1jeqB/ include read-alignments.under InFilePrefix t0187-301-417/1jeyB/ include read-alignments.under InFilePrefix t0187-301-417/1xlmA/ include read-alignments.under InFilePrefix t0187-301-417/1xlaA/ include read-alignments.under InFilePrefix t0187-301-417/1gowA/ include read-alignments.under InFilePrefix InFilePrefix // 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 0.05 \ ClashingRotamer 0.5 \ OneRotamer 0.001 \ InsertFragment 10 \ CrossAndInsert 10 \ CrossOver 0\ TwoFragment 10 \ InsertSpecificFragment 15 \ ReduceBreak 0.5 \ CloseGap 0.1 \ ReduceClash 1 \ JiggleSubtree 1 \ OptSubtree 1 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0187.try3 OptConform pool_size 40 num_gen 20 gen_size 180 super_iter 5 \ pdb use_all no_initial_fill scwrl_each NameConform T0187.try3-opt PrintConformPDB T0187.try3-opt.pdb edges SCWRLConform NameConform T0187.try3-opt-scwrl PrintConformPDB T0187.try3-opt-scwrl.pdb CostConform Time quit