// To be run from pce/casp5/t0173 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ //ConformFromSeq replace // get a random conformation, removing all-zero one //NameConform T0173.rand //Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0173.t2k.undertaker-align.script ReadFragmentAlignment T0173.t2k-2track-undertaker.a2m InfilePrefix 1e0tA/ include read-alignments.under InfilePrefix 1edt/ include read-alignments.under InfilePrefix 6mhtA/ include read-alignments.under InfilePrefix 1hmy/ include read-alignments.under InfilePrefix 2ebn/ include read-alignments.under InfilePrefix 3mhtA/ include read-alignments.under InfilePrefix 1lvk/ include read-alignments.under InfilePrefix 1fjxA/ include read-alignments.under InfilePrefix 1f6dA/ include read-alignments.under InfilePrefix 1db3A/ include read-alignments.under InfilePrefix 1d0yA/ include read-alignments.under InfilePrefix Time InfilePrefix decoys/ // ReadConformPDB T0173.try5-al8+T0173-2ebn-2track-protein-STR-global-adpstyle1.pw.a2m.gz:2ebn.7.40.pdb // NameConform T0173.try7-try5-7 // ReadConformPDB T0173.try5-al10.8.40.pdb // NameConform T0173.try7-try5-8 // ReadConformPDB T0173.try5-al10.3.40.pdb // NameConform T0173.try7-try5-3 // ReadConformPDB T0173.try6.8.40.pdb // NameConform T0173.try7-try6-8 // ReadConformPDB T0173.try5-al8+T0173-2ebn-2track-protein-STR-global-adpstyle1.pw.a2m.gz:2ebn.7.40.pdb // NameConform T0173.try8-try5-7 // ReadConformPDB T0173.try5-al10.8.40.pdb // NameConform T0173.try8-try5-8 // ReadConformPDB T0173.try5-al10.3.40.pdb // NameConform T0173.try8-try5-3 // ReadConformPDB T0173.try6.8.40.pdb // NameConform T0173.try8-try6-8 // ReadConformPDB T0173.try6-al6.9.40.pdb // NameConform T0173.try8-try6-9 // ReadConformPDB T0173.try6-opt-scwrl.pdb // NameConform T0173.try8-try6 // ReadConformPDB T0173.try8-opt-scwrl.pdb // NameConform T0173.try9-try8 // ReadConformPDB T0173.try8-try5-7.0.40.pdb // NameConform T0173.try9-try8-0 // ReadConformPDB T0173.try8-try5-7.1.40.pdb // NameConform T0173.try9-try8-1 // ReadConformPDB T0173.try8-try5-7.3.40.pdb // NameConform T0173.try9-try8-3 // ReadConformPDB T0173.try5-al10.3.40.pdb // NameConform T0173.try9-try5-3 InfilePrefix // ReadConformPDB decoys/T0173.try9-opt-scwrl.pdb // NameConform T0173.try11-try9 // ReadConformPDB decoys/T0173.try10-opt-scwrl.pdb // NameConform T0173.try11-try10 // ReadConformPDB decoys/T0173.try4-opt-scwrl.pdb // nameConform T0173.try12-try4 //ReadConformPDB decoys/T0173.try12.0.120.pdb // nameConform T0173.try15-try12-0 //ReadConformPDB decoys/T0173.try13-opt-scwrl.pdb // nameConform T0173.try15-try13 //ReadConformPDB decoys/T0173.try14-opt-scwrl.pdb // nameConform T0173.try15-try13 //ReadConformPDB decoys/T0173.try11-opt.pdb // nameConform T0173.try11-try16 //ReadConformPDB decoys/T0173.try14-opt-scwrl.pdb // nameConform T0173.try14-try16 //ReadConformPDB decoys/T0173.try15.3.100.pdb // nameConform T0173.try15-try16 // ReadConformPDB decoys/T0173.try17-opt-scwrl.pdb // nameConform T0173.try18-try17 // ReadConformPDB decoys/T0173.try18.2.100.pdb // nameConform T0173.try19-try18-2 // ReadConformPDB decoys/T0173.try18.1.100.pdb // nameConform T0173.try19-try18-1 // ReadConformPDB decoys/T0173.try17-opt-scwrl.pdb // nameConform T0173.try19-try17 // ReadConformPDB decoys/T0173.try11-opt.pdb // nameConform T0173.try20-try11 // ReadConformPDB decoys/T0173.try10-opt-scwrl.pdb // nameConform T0173.try20-try10 // ReadConformPDB decoys/T0173.try11-opt.pdb // nameConform T0173.try21-try11 // ReadConformPDB decoys/T0173.try10-opt-scwrl.pdb // nameConform T0173.try21-try10 // ReadConformPDB decoys/T0173.try11-try9.1.120.pdb // nameConform T0173.try22-try11-1 // ReadConformPDB decoys/T0173.try10-opt-scwrl.pdb // nameConform T0173.try22-try10 // ReadConformPDB decoys/T0173.try21-opt.pdb // nameConform T0173.try22-try21 // ReadConformPDB decoys/T0173.try21-opt-scwrl.pdb // nameConform T0173.try22-try21-s // ReadConformPDB decoys/T0173.try11-try9.1.120.pdb // nameConform T0173.try23-try11-1 // ReadConformPDB decoys/T0173.try10-opt-scwrl.pdb // nameConform T0173.try23-try10 // ReadConformPDB decoys/T0173.try21-opt.pdb // nameConform T0173.try23-try21 // ReadConformPDB decoys/T0173.try21-opt-scwrl.pdb // nameConform T0173.try23-try21-s // ReadConformPDB decoys/T0173.try22-opt.pdb // nameConform T0173.try23-try22 ReadConformPDB decoys/T0173.try22-opt.pdb nameConform T0173.try24-try22 ReadConformPDB decoys/T0173.try23-opt-scwrl.pdb nameConform T0173.try24-try23 ReportCost undertaker-try24.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0173.try14-al2 // PrintConformPDB T0173.try14-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0173.try14-al4 // PrintConformPDB T0173.try14-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0173.try14-al6 // PrintConformPDB T0173.try14-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0173.try14-al8 // PrintConformPDB T0173.try14-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0173.try14-al10 // PrintConformPDB T0173.try14-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0173.try14-al12 // PrintConformPDB T0173.try14-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 T0173.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 // InsertFragment cranked up to 10 from 3 after move // OptSubtree cranked up to 0.2 from 0.4 after move InitMethodProbs InsertAlignment 0.1 \ ClashingRotamer 0.5 \ OneRotamer 0.01 \ InsertFragment 3 \ CrossAndInsert 8 \ CrossOver 0 \ TwoFragment 10 \ InsertSpecificFragment 8 \ ReduceBreak 1 \ ReduceConstraint 5 \ CloseGap 0.1 \ ReduceClash 1 \ JiggleSubtree 0.02 \ OptSubtree 0.2 \ InsertSSBond 0 \ ImproveSSBond 0 // num_gen down to 20 from 100 for move try // no_initial_fill added " " NameConform T0173.try24 OptConform pool_size 50 num_gen 100 gen_size 150 super_iter 1 \ use_all pdb // scwrl_each NameConform T0173.try24-opt PrintConformPDB T0173.try24-opt.pdb edges SCWRLConform NameConform T0173.try24-opt-scwrl PrintConformPDB T0173.try24-opt-scwrl.pdb CostConform Time quit