// To be run from pce/casp5/t0135 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0135.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0135.t2k.undertaker-align.script ReadFragmentAlignment T0135.t2k-2track-undertaker.a2m // The following alignments are from structural alignments by VAST // to try7-opt. A few were edited in Cn3D to extend the alignments. ReadFragmentAlignment T0135-2bopA-edited.vast.fasta ReadFragmentAlignment T0135-1h6kZ-edited.vast.fasta ReadFragmentAlignment T0135-1qm9A-edited.vast.fasta ReadFragmentAlignment T0135-1gh8A-edited.vast.fasta ReadFragmentAlignment T0135-2bopA.vast.fasta ReadFragmentAlignment T0135-1qupA.vast.fasta ReadFragmentAlignment T0135-1fj7A.vast.fasta ReadFragmentAlignment T0135-1cpzA.vast.fasta ReadFragmentAlignment T0135-1dq3A.vast.fasta ReadFragmentAlignment T0135-1f9fD.vast.fasta ReadFragmentAlignment T0135-1qm9A.vast.fasta ReadFragmentAlignment T0135-1a7gE.vast.fasta ReadFragmentAlignment T0135-1by9.vast.fasta // The following alignments were edited from the top 2 VAST alignments // from one of the early iterations of try14. ReadFragmentAlignment T0135-1mroA-edited14.vast.fasta ReadFragmentAlignment T0135-2bopA-edited14.vast.fasta Time // ReadConformPDB decoys/T0135.try4-opt.pdb // NameConform T0135.try7-try4 // ReadConformPDB decoys/T0135.try9-opt-scwrl.pdb // NameConform try10-try9 // ReadConformPDB decoys/T0135.try9.22.40.pdb // NameConform try10-try9-22 // ReadConformPDB decoys/T0135.try7-opt.pdb // NameConform T0135.try11-try7 // ReadConformPDB decoys/T0135.try9-opt-scwrl.pdb // NameConform T0135.try11-try9 // ReadConformPDB decoys/T0135.try10-opt-scwrl.pdb // NameConform T0135.try11-try10 // ReadConformPDB decoys/T0135-cut-and-paste.pdb // NameConform T0135.try12-cut // ReadConformPDB decoys/T0135.try12-opt-scwrl.pdb // NameConform T0135.try13-try12 // ReadConformPDB decoys/T0135-cut-and-paste-2.pdb // NameConform T0135.try14-cut // ReadConformPDB decoys/T0135-cut-and-paste-3.pdb // NameConform T0135.try18-cut // ReadConformPDB decoys/T0135.try17-opt.pdb // NameConform T0135.try19-try17 // ReadConformPDB decoys/T0135.try18-opt.pdb // NameConform T0135.try19-try18 // ReadConformPDB decoys/T0135.try19.2.40.pdb // NameConform T0135.try20-try19 // ReadConformPDB decoys/T0135.try20-opt-scwrl.pdb // NameConform T0135.try21-try20 // ReadConformPDB decoys/T0135.try21-opt.pdb // NameConform T0135.try22-try21 // ReadConformPDB decoys/T0135.try22.0.40.pdb // NameConform T0135.try23-try22-0 // ReadConformPDB decoys/T0135.try22.4.40.pdb // NameConform T0135.try23-try22-4 // ReadConformPDB decoys/T0135.try22.1.40.pdb // NameConform T0135.try23-try22-1 // ReadConformPDB decoys/T0135.try23-opt.pdb // NameConform T0135.try24-try23 // ReadConformPDB decoys/T0135.try23.16.40.pdb // NameConform T0135.try24-try23-16 // ReadConformPDB decoys/T0135.try23.17.40.pdb // NameConform T0135.try24-try23-17 // ReadConformPDB decoys/T0135.try23-opt.pdb // NameConform T0135.try25-try23 // ReadConformPDB decoys/T0135.try24-opt.pdb // NameConform T0135.try25-try24 // ReadConformPDB decoys/T0135.try24-opt-scwrl.pdb // NameConform T0135.try25-try24-s // ReadConformPDB decoys/T0135.try24-try23.18.40.pdb // NameConform T0135.try25-try24-18 // SCWRLConform // NameConform T0135.try25 // ReadConformPDB decoys/T0135.try25-opt.pdb // NameConform T0135.try26-try25 // ReadConformPDB decoys/T0135.try24-opt.pdb // NameConform T0135.try26-try24 ReadConformPDB decoys/T0135-cut-and-paste-4.pdb NameConform T0135.try27 ReportCost undertaker-try27.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0135.try27-al2 // PrintConformPDB T0135.try27-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0135.try27-al4 // PrintConformPDB T0135.try27-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0135.try27-al6 // PrintConformPDB T0135.try27-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0135.try27-al8 // PrintConformPDB T0135.try27-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0135.try27-al10 // PrintConformPDB T0135.try27-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0135.try27-al12 // PrintConformPDB T0135.try27-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 T0135.t2k.frag OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0.1 \ ClashingRotamer 0.5 \ InsertFragment 1 \ Crossover 0.1 \ CrossAndInsert 2 \ TwoFragment 0.5 \ InsertSpecificFragment 0.5 \ ReduceBreak 5 \ CloseGap 0.3 \ ReduceClash 1 \ ReduceConstraint 0.5 \ JiggleSubtree 0.3 \ OptSubtree 0.2 \ InsertSSBond 0 \ ImproveSSBond 0 OptConform pool_size 50 num_gen 40 gen_size 100 super_iter 20 \ pdb scwrl_each use_all NameConform T0135.try27-opt PrintConformPDB T0135.try27-opt.pdb edges OptimizeRotamers iter 5 conform_per_iter 100 rdb NameConform T0135.try27-opt-rot PrintConformPDB T0135.try27-opt-rot.pdb SCWRLConform NameConform T0135.try27-opt-scwrl PrintConformPDB T0135.try27-opt-scwrl.pdb CostConform Time quit