// 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.try3-robetta2.1.60.pdb NameConform T0146.try26-model1 ReportCost undertaker-try26.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.try26-al2 // PrintConformPDB T0146.try26-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0146.try26-al4 // PrintConformPDB T0146.try26-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0146.try26-al6 // PrintConformPDB T0146.try26-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0146.try26-al8 // PrintConformPDB T0146.try26-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0146.try26-al10 // PrintConformPDB T0146.try26-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0146.try26-al12 // PrintConformPDB T0146.try26-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.try26 OptConform pool_size 40 num_gen 20 gen_size 80 super_iter 5 \ pdb use_all // scwrl_each NameConform T0146.try26-opt PrintConformPDB T0146.try26-opt.pdb edges SCWRLconform NameConform T0146.try26-opt-scwrl PrintConformPDB T0146.try26-opt-scwrl.pdb CostConform Time quit