// To be run from pce/casp5/t0146 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms Include T0146.t2k.undertaker-align.script ReadFragmentAlignment T0146.t2k-2track-undertaker.a2m //include read-subdomain.under Time // ReadConformPDB robetta1.pdb.gz // Nameconform T0146.try3-robetta1 // ReadConformPDB robetta2.pdb.gz // Nameconform T0146.try3-robetta2 // ReadConformPDB robetta3.pdb.gz // Nameconform T0146.try3-robetta3 // ReadConformPDB robetta4.pdb.gz // Nameconform T0146.try3-robetta4 // ReadConformPDB robetta5.pdb.gz // Nameconform T0146.try3-robetta5 // ReadConformPDB decoys/T0146.try4-opt-scwrl.pdb // NameConform T0146.try5-try4 // ReadConformPDB decoys/T0146.try3-opt.pdb // NameConform T0146.try5-try3 // ReadConformPDB robetta1.pdb.gz // Nameconform T0146.try6-robetta1 // ReadConformPDB robetta2.pdb.gz // Nameconform T0146.try6-robetta2 // ReadConformPDB robetta3.pdb.gz // Nameconform T0146.try6-robetta3 // ReadConformPDB robetta4.pdb.gz // Nameconform T0146.try6-robetta4 // ReadConformPDB robetta5.pdb.gz // Nameconform T0146.try6-robetta5 //ReadConformPDB decoys/T0146.try4-opt.pdb // NameConform T0146.try17-try4 //ReadConformPDB decoys/T0146.try6-opt-scwrl.pdb // NameConform T0146.try17-try6 //ReadConformPDB decoys/T0146.try7-opt-scwrl.pdb // NameConform T0146.try17-try7 //ReadConformPDB decoys/T0146.try8-opt-scwrl.pdb // NameConform T0146.try17-try8 // ReadConformPDB decoys/T0146.try16-try15-moved.pdb // NameConform T0146.try17-try16-moved // ReadConformPDB decoys/T0146-robetta-moved.pdb // NameConform T0146.try17-T0146-robetta-moved.pdb // ReadConformPDB decoys/T0146.try17-opt.pdb // NameConform T0146.try18-try17 //ReadConformPDB decoys/T0146.try16-opt.pdb // NameConform T0146.try23-try16 //ReadConformPDB decoys/T0146.try17-opt.pdb // NameConform T0146.try23-try17 //ReadConformPDB decoys/T0146.try17-try16-moved.7.40.pdb // NameConform T0146.try23-try17-7 //ReadConformPDB decoys/T0146.try18.1.80.pdb // NameConform T0146.try23-try18-1 //ReadConformPDB decoys/T0146.try18.0.80.pdb // NameConform T0146.try23-try18-0 //for try23, adding all good-scoring models from the //initial conformations of trys 20 & 21 (hoping to //fix the strand-13-as-helix problem... ReadConformPDB decoys/T0146.try18.3.80.pdb NameConform T0146.try23-try18-3 ReadConformPDB decoys/T0146.try21.0.80.pdb NameConform T0146.try23-try21.0 ReadConformPDB decoys/T0146.try20-try17-7.2.80.pdb NameConform T0146.try23-try20.7-2 ReadConformPDB decoys/T0146.try20-try17.0.80.pdb NameConform T0146.try23-try20.0 ReadConformPDB decoys/T0146.try20-try17.1.80.pdb NameConform T0146.try23-try21.1 ReadConformPDB decoys/T0146.try20-try17.3.80.pdb NameConform T0146.try23-try21.3 ReadConformPDB decoys/T0146.try21.0.80.pdb NameConform T0146.try23-try21.0 ReadConformPDB decoys/T0146.try21.1.80.pdb NameConform T0146.try23-try21.1 ReadConformPDB decoys/T0146.try21.2.80.pdb NameConform T0146.try23-try21.2 ReportCost undertaker-try23.rdb // ConformFromSeq replace // get a random conformation, removing all-zero one // NameConform T0146.rand // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0146.try23-al2 // PrintConformPDB T0146.try23-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0146.try23-al4 // PrintConformPDB T0146.try23-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0146.try23-al6 // PrintConformPDB T0146.try23-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0146.try23-al8 // PrintConformPDB T0146.try23-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0146.try23-al10 // PrintConformPDB T0146.try23-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0146.try23-al12 // PrintConformPDB T0146.try23-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 T0146.t2k.frag ReadFragmentAlignment t0146-1-80/T0146.t2k.frag ReadFragmentAlignment t0146-1-180/T0146.t2k.frag ReadFragmentAlignment t0146-120-220/T0146.t2k.frag ReadFragmentAlignment t0146-180-325/T0146.t2k.frag OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0.3 \ ClashingRotamer 0.5 \ InsertFragment 10 \ CrossAndInsert 2 \ CrossOver 0 \ TwoFragment 1 \ InsertSpecificFragment 5 \ ReduceBreak 0.5 \ CloseGap 0.1 \ OptSubtree 0.03 \ JiggleSubtree 0.03 \ ReduceConstraint 1 \ ReduceClash 1 \ InsertSSBond 0 NameConform T0146.try23 OptConform pool_size 40 num_gen 10 gen_size 80 super_iter 5 pdb use_all // scwrl_each NameConform T0146.try23-opt PrintConformPDB T0146.try23-opt.pdb edges SCWRLconform NameConform T0146.try23-opt-scwrl PrintConformPDB T0146.try23-opt-scwrl.pdb CostConform Time quit