// To be run from pce/casp5/t0169 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0169.rand Time InFilePrefix ReadTemplateAtoms Template.atoms ReadFragmentAlignment T0169-1qsmA.vast.a2m // ReadConformPDB decoys/T0169.try20-opt.pdb // NameConform T0169.try21-try20 // TryAllAlign shrink 0.1 min_keep_length 3 // NameConform T0169.try21-try20-al1 // TryAllAlign shrink 0 min_keep_length 1 // NameConform T0169.try21-try20-al2 // ReadConformPDB decoys/T0169.try17-opt.pdb // NameConform T0169.try21-try17 // TryAllAlign shrink 0.1 min_keep_length 3 // NameConform T0169.try21-try17-al1 // TryAllAlign shrink 0 min_keep_length 1 // NameConform T0169.try21-try17-al2 // ReadConformPDB decoys/T0169.try16-opt.pdb // NameConform T0169.try21-try16 // TryAllAlign shrink 0.1 min_keep_length 3 // NameConform T0169.try21-try16-al1 // TryAllAlign shrink 0 min_keep_length 1 // NameConform T0169.try21-try16-al2 // ReadConformPDB decoys/T0169.try9-opt-scwrl.pdb // NameConform T0169.try21-try9 // TryAllAlign shrink 0.1 min_keep_length 3 // NameConform T0169.try21-try9-al1 // TryAllAlign shrink 0 min_keep_length 1 // NameConform T0169.try21-try9-al2 // ReadConformPDB decoys/T0169.try7-opt.pdb // NameConform T0169.try21-try7 // TryAllAlign shrink 0.1 min_keep_length 3 // NameConform T0169.try21-try7-al1 // TryAllAlign shrink 0 min_keep_length 1 // NameConform T0169.try21-try7-al2 // ReadConformPDB decoys/T0169.try6-opt.pdb // NameConform T0169.try21-try6 // TryAllAlign shrink 0.1 min_keep_length 3 // NameConform T0169.try21-try6-al1 // TryAllAlign shrink 0 min_keep_length 1 // NameConform T0169.try21-try6-al2 ReadFragmentAlignment T0169-1b87A.vast.a2m Include T0169.t2k.undertaker-align.script ReadFragmentAlignment T0169.t2k-2track-undertaker.a2m InfilePrefix 1i1dA/ include read-alignments.under InfilePrefix 1i12A/ include read-alignments.under InfilePrefix 1i21A/ include read-alignments.under InfilePrefix 1qsmA/ include read-alignments.under InfilePrefix 1cjwA/ include read-alignments.under InfilePrefix 1bo4A/ include read-alignments.under InfilePrefix 1b87A/ include read-alignments.under InfilePrefix 1bo4B/ include read-alignments.under InfilePrefix InfilePrefix 1qstA/ include read-alignments.under InfilePrefix 1qsoA/ include read-alignments.under InfilePrefix 1yghA/ include read-alignments.under InfilePrefix 1b6bA/ include read-alignments.under InfilePrefix 1kuxA/ include read-alignments.under InfilePrefix 1ib1E/ include read-alignments.under InfilePrefix 1qsrA/ include read-alignments.under InfilePrefix 5gcnA/ include read-alignments.under InfilePrefix 1cm0A/ include read-alignments.under InfilePrefix 1nmtA/ include read-alignments.under InfilePrefix Time // ReadConformPDB decoys/T0169.try5-opt.pdb // NameConform T0169.try5-try6 // ReadConformPDB decoys/T0169.try2-opt.pdb // NameConform T0169.try7-try2 // ReadConformPDB decoys/T0169.try5-opt.pdb // NameConform T0169.try7-try5 // ReadConformPDB decoys/T0169.try6-opt.pdb // NameConform T0169.try7-try6 // ReadConformPDB decoys/T0169.try4-opt.pdb // NameConform T0169.try7-try4 // ReadConformPDB decoys/T0169.try7-opt.pdb // NameConform T0169.try8-try7 // ReadConformPDB decoys/T0169.try8-opt.pdb // NameConform T0169.try9-try8 // ReadConformPDB decoys/T0169.try9-opt.pdb // NameConform T0169.try10-try9 // ReadConformPDB decoys/T0169.try9.6.100.pdb // NameConform T0169.try10-try9-6 // ReadConformPDB decoys/T0169.try9.1.100.pdb // NameConform T0169.try10-try9-1 // ReadConformPDB decoys/T0169.try9.3.100.pdb // NameConform T0169.try10-try9-3 // ReadConformPDB decoys/T0169.try9.0.100.pdb // NameConform T0169.try10-try9-0 // ReadConformPDB decoys/T0169.try3-al8.pdb // NameConform T0169.try11-try3-al8 // ReadConformPDB decoys/T0169.try8-al6+1i21A-T0169-vit-adpstyle5.pw.a2m.gz:1i21A.0.100.pdb // NameConform T0169.try11-try8-0 // ReadConformPDB decoys/T0169.try9.3.100.pdb // NameConform T0169.try11-try9-3 // ReadConformPDB decoys/T0169.try10.8.100.pdb // NameConform T0169.try11-try10-8 // ReadConformPDB decoys/T0169.try10-opt.pdb // NameConform T0169.try11-try10 // ReadConformPDB decoys/T0169.try10.2.100.pdb // NameConform T0169.try11-try10-2 // ReadConformPDB decoys/T0169.try11.7.120.pdb // NameConform T0169.try12-try11-7 // ReadConformPDB decoys/T0169.try11.5.120.pdb // NameConform T0169.try12-try11-5 // ReadConformPDB decoys/T0169.try11.6.120.pdb // NameConform T0169.try12-try11-6 // ReadConformPDB decoys/T0169.try11.9.120.pdb // NameConform T0169.try12-try11-9 // ReadConformPDB decoys/T0169.try10-opt.pdb // NameConform T0169.try12-try10 // ReadConformPDB decoys/T0169.try11.7.120.pdb // NameConform T0169.try13-try11-7 // ReadConformPDB decoys/T0169.try11.5.120.pdb // NameConform T0169.try13-try11-5 // ReadConformPDB decoys/T0169.try10-opt.pdb // NameConform T0169.try13-try10 // ReadConformPDB decoys/T0169.try9.0.100.pdb // NameConform T0169.try13-try9-0 // ReadConformPDB decoys/T0169.try5-try6.10.100.pdb // NameConform T0169.try13-try6-10 // ReadConformPDB decoys/T0169.try13-opt.pdb // NameConform T0169.try14-try13 // ReadConformPDB decoys/T0169.try13-try11-7.6.60.pdb // NameConform T0169.try14-try13-6 // ReadConformPDB decoys/T0169.try13-try11-7.1.60.pdb // NameConform T0169.try14-try13-1 // ReadConformPDB decoys/T0169.try10.5.100.pdb // NameConform T0169.try15-try10-5 // ReadConformPDB decoys/T0169.try14-opt.pdb // NameConform T0169.try15-try14 // ReadConformPDB decoys/T0169.try14.4.80.pdb // NameConform T0169.try15-try14-4 // ReadConformPDB decoys/T0169.try13-try11-7.1.60.pdb // NameConform T0169.try15-try13-1 // ReadConformPDB decoys/T0169.try10.5.100.pdb // NameConform T0169.try16-try10-5 // ReadConformPDB decoys/T0169.try13-opt.pdb // NameConform T0169.try16-try13 // ReadConformPDB decoys/T0169.try14.4.80.pdb // NameConform T0169.try16-try14-4 // ReadConformPDB decoys/T0169.try13-try11-7.1.60.pdb // NameConform T0169.try16-try13-1 // ReadConformPDB decoys/T0169.try14-opt.pdb // NameConform T0169.try16-try14 // ReadConformPDB decoys/T0169.try10.0.100.pdb // NameConform T0169.try17-try10-0 // ReadConformPDB decoys/T0169.try13-try11-7.6.60.pdb // NameConform T0169.try17-try13-6 // ReadConformPDB decoys/T0169.try14.4.80.pdb // NameConform T0169.try17-try14-4 // ReadConformPDB decoys/T0169.try15-opt.pdb // NameConform T0169.try17-try15 // ReadConformPDB decoys/T0169.try16-opt.pdb // NameConform T0169.try17-try16 // ReadConformPDB decoys/T0169.try12-try11-5.7.120.pdb // NameConform T0169.try18-try12-7 // ReadConformPDB decoys/T0169.try17-opt.pdb // NameConform T0169.try18-try17 // ReadConformPDB decoys/T0169.try4.15.60.pdb // NameConform T0169.try18-try4-15200 // ReadConformPDB decoys/T0169.try12-try11-5.7.120.pdb // NameConform T0169.try19-try12-7 // ReadConformPDB decoys/T0169.try4.15.60.pdb // NameConform T0169.try19-try4-15 // ReadConformPDB decoys/T0169.try4.12.60.pdb // NameConform T0169.try19-try4-12 // ReadConformPDB decoys/T0169.try17-opt.pdb // NameConform T0169.try19-try17 // ReadConformPDB decoys/T0169.try18.0.100.pdb // NameConform T0169.try19-try18-0 // ReadConformPDB decoys/T0169.try18.1.100.pdb // NameConform T0169.try19-try18-1 // ReadConformPDB decoys/T0169.try18.2.100.pdb // NameConform T0169.try19-try18-2 // ReadConformPDB decoys/T0169.try18.3.100.pdb // NameConform T0169.try19-try18-3 // ReadConformPDB decoys/T0169.try7-opt.pdb // NameConform T0169.try20-try7 // ReadConformPDB decoys/T0169.try10.5.100.pdb // NameConform T0169.try20-try10-5 // ReadConformPDB decoys/T0169.try13-opt-scwrl.pdb // NameConform T0169.try22-try13 // ReadConformPDB decoys/T0169.try14-opt.pdb // NameConform T0169.try22-try14 // ReadConformPDB decoys/T0169.try8-opt.pdb // NameConform T0169.try23-try8 // ReadConformPDB decoys/T0169.try10-opt.pdb // NameConform T0169.try23-try10 // ReadConformPDB decoys/T0169.try11-opt.pdb // NameConform T0169.try23-try11 // ReadConformPDB decoys/T0169.try13-try11-7.3.60.pdb // NameConform T0169.try23-try13-3 // ReadConformPDB decoys/T0169.try12-opt.pdb // NameConform T0169.try23-try12 // ReadConformPDB decoys/T0169.try14-try13.1.80.pdb // NameConform T0169.try23-try14-1 // ReadConformPDB decoys/T0169.try14-opt.pdb // NameConform T0169.try23-try14 // ReadConformPDB decoys/T0169.try22-opt.pdb // NameConform T0169.try23-try22 // ReadConformPDB decoys/T0169.try8-opt.pdb // NameConform T0169.try24-try8 // ReadConformPDB decoys/T0169.try10-opt.pdb // NameConform T0169.try24-try10 // ReadConformPDB decoys/T0169.try11.5.120.pdb // NameConform T0169.try24-try11-5 // ReadConformPDB decoys/T0169.try12-opt.pdb // NameConform T0169.try24-try12 // ReadConformPDB decoys/T0169.try15-try14-4.2.80.pdb // NameConform T0169.try24-try15-2 // ReadConformPDB decoys/T0169.try17-try15.2.80.pdb // NameConform T0169.try24-try17-2 // ReadConformPDB decoys/T0169.try13-try11-7.3.60.pdb // NameConform T0169.try24-try13-3 // ReadConformPDB decoys/T0169.try14-opt-scwrl.pdb // NameConform T0169.try24-try14 // ReadConformPDB decoys/T0169.try22-opt.pdb // NameConform T0169.try24-try22 // ReadConformPDB decoys/T0169.try23-opt.pdb // NameConform T0169.try24-try23 // ReadconformPDB decoys/T0169-moved.pdb // NameConform T0169.try25-moved // ReadconformPDB decoys/T0169.try11.7.120.pdb // NameConform T0169.try26-try11-7 // ReadconformPDB decoys/T0169.try12-opt.pdb // NameConform T0169.try26-try12 // ReadconformPDB decoys/T0169.try12-try11-5.10.120.pdb // NameConform T0169.try26-try12-10 // ReadconformPDB decoys/T0169.try12-try11-5.1.120.pdb // NameConform T0169.try26-try12-1 // readConformPDB decoys/T0169.try26-opt.pdb // NameConform T0169.try27-try26 // readConformPDB decoys/T0169.try26-opt.pdb // NameConform T0169.try28-try26 // readConformPDB decoys/T0169.try27.0.120.pdb // NameConform T0169.try28-try27-0 // readConformPDB decoys/T0169.try27.1.120.pdb // NameConform T0169.try28-try27-1 // readConformPDB decoys/T0169.try27-opt.pdb // NameConform T0169.try28-try27 ReadconformPDB decoys/T0169.try12-try11-5.1.120.pdb NameConform T0169.try29-try12-1 readConformPDB decoys/T0169.try26-opt.pdb NameConform T0169.try29-try26 readConformPDB decoys/T0169.try27-opt.pdb NameConform T0169.try29-try27 readConformPDB decoys/T0169.try28-opt.pdb NameConform T0169.try29-try28 ReportCost undertaker-try29.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0169.try29-al2 // PrintConformPDB T0169.try29-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0169.try29-al4 // PrintConformPDB T0169.try29-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0169.try29-al6 // PrintConformPDB T0169.try29-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0169.try29-al8 // PrintConformPDB T0169.try29-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0169.try29-al10 // PrintConformPDB T0169.try29-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0169.try29-al12 // PrintConformPDB T0169.try29-al12.pdb edges CostConform Time // ReadConformPDB decoys/T0169.try1-opt.pdb // NameConform T0169.try1-try3 // ReadConformPDB decoys/T0169.try2-opt.pdb // NameConform T0169.try2-try3 // The following alignments are not as good as the ones tried above, // so are not used in getting the starting point. InFilePrefix ReadFragmentAlignment T0169.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 InitMethodProbs InsertAlignment 0.1 \ ClashingRotamer 0.5 \ oneRotamer 0.1 \ InsertFragment 10 \ CrossAndInsert 10 \ CrossOver 0 \ TwoFragment 4 \ InsertSpecificFragment 5 \ ReduceBreak 1 \ CloseGap 0.2 \ ReduceClash 1 \ ReduceConstraint 1 \ JiggleSubtree 0.01 \ OptSubtree 0.05 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0169.try29 OptConform pool_size 40 num_gen 300 gen_size 180 super_iter 1 \ pdb use_all // no_initial_fill // scwrl_each NameConform T0169.try29-opt PrintConformPDB T0169.try29-opt.pdb edges SCWRLConform NameConform T0169.try29-opt-scwrl PrintConformPDB T0169.try29-opt-scwrl.pdb CostConform Time quit