// To be run from pce/casp5/t0156 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0156.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0156.t2k.undertaker-align.script ReadFragmentAlignment T0156.t2k-2track-undertaker.a2m InfilePrefix 1ja9A/ include read-alignments.under InfilePrefix 1ldg/ include read-alignments.under // InfilePrefix 1kpjI/ // include read-alignments.under InfilePrefix 1gpjA/ include read-alignments.under InfilePrefix 1bvp1/ include read-alignments.under InfilePrefix 1jhdA/ include read-alignments.under InfilePrefix 1sayA/ include read-alignments.under InfilePrefix 1ceqA/ include read-alignments.under InfilePrefix 1pjbA/ include read-alignments.under InfilePrefix 1hg3A/ include read-alignments.under inFilePrefix // ReadConformPDB decoys/T0156.try8+T0156-1ja9A-vit-adp...+T0156-1ja9A-2track-protein-EBGHTL-global-adpstyle1.pw.a2m.gz:1ja9A.30.60.pdb // NameConform T0156.try9-try8-30 // ReadConformPDB decoys/T0156.try8+T0156-1sayA-2track-...+T0156-1ja9A-2track-protein-EBGHTL-local-adpstyle5.pw.a2m.gz:1ja9A.27.60.pdb // NameConform T0156.try9-try8-27 // ReadConformPDB decoys/T0156.try6-al8+T0156-1ja9A-2tr...+T0156-1ja9A-2track-protein-STR-local-adpstyle5.pw.a2m.gz:1ja9A.19.30.pdb // NameConform T0156.try9-try6-19 // ReadConformPDB decoys/T0156.try6-opt-scwrl.pdb // NameConform T0156.try9-try6 // ReadConformPDB decoys/T0156.try8+T0156-1pjbA-2track-...+T0156-1ja9A-2track-protein-STR-global-adpstyle1.pw.a2m.gz:1ja9A.18.60.pdb // NameConform T0156.try9-try8-18 // ReadConformPDB decoys/T0156.try9.1.60.pdb // NameConform T0156.try10-try9-1 // ReadConformPDB decoys/T0156.try9.2.60.pdb // NameConform T0156.try10-try9-2 // ReadConformPDB decoys/T0156.try9.3.60.pdb // NameConform T0156.try10-try9-3 // ReadConformPDB decoys/T0156.try9.8.60.pdb // NameConform T0156.try10-try9-8 // ReadConformPDB decoys/T0156.try9.6.60.pdb // NameConform T0156.try10-try9-6 // ReadConformPDB decoys/T0156.try9.7.60.pdb // NameConform T0156.try10-try9-7 // ReadConformPDB decoys/T0156.try9.9.60.pdb // NameConform T0156.try10-try9-9 // ReadConformPDB decoys/T0156.try9.0.60.pdb // NameConform T0156.try10-try9-0 // ReadConformPDB decoys/T0156.try9.4.60.pdb // NameConform T0156.try10-try9-4 // ReadConformPDB decoys/T0156.try9.5.60.pdb // NameConform T0156.try10-try9-5 // ReadConformPDB decoys/T0156.try11-opt-scwrl.pdb // NameConform T0156.try12-try11 // ReadConformPDB decoys/T0156.try10-opt-scwrl.pdb // NameConform T0156.try12-try10 // ReadConformPDB decoys/T0156.try12-opt-scwrl.pdb // NameConform T0156.try13-try12 // ReadConformPDB decoys/T0156-moved.pdb // NameConform T0156.try14 // ReadConformPDB decoys/T0156.try14-opt.pdb // NameConform T0156.try15-try14 PopConform // get rid of random conformation // ReadConformPDB decoys/T0156.cut-and-paste.pdb // NameConform T0156.try18 // ReadConformPDB decoys/T0156.cut-and-paste.pdb // NameConform T0156.try19 // ReadConformPDB decoys/T0156.cut-and-paste.pdb // NameConform T0156.try20 // ReadConformPDB decoys/T0156.try19-opt.pdb // NameConform T0156.try21-try19 ReadConformPDB decoys/T0156.try20-opt-scwrl.pdb NameConform T0156.try22-try20 Time ReportCost undertaker-try22.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0156.try22-al2 // PrintConformPDB T0156.try22-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0156.try22-al4 // PrintConformPDB T0156.try22-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0156.try22-al6 // PrintConformPDB T0156.try22-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0156.try22-al8 // PrintConformPDB T0156.try22-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0156.try22-al10 // PrintConformPDB T0156.try22-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0156.try22-al12 // PrintConformPDB T0156.try22-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 T0156.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 \ ClashingRotamer 0.5 \ InsertFragment 9 \ CrossAndInsert 2 \ TwoFragment 1 \ InsertSpecificFragment 4 \ ReduceBreak 5 \ CloseGap 0.1 \ JiggleSubtree 0.03 \ OptSubtree 0.03 \ ReduceClash 1 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0156.try22 OptConform pool_size 70 num_gen 40 gen_size 200 super_iter 10 \ scwrl_each use_all pdb NameConform T0156.try22-opt PrintConformPDB T0156.try22-opt.pdb edges SCWRLConform NameConform T0156.try22-opt-scwrl PrintConformPDB T0156.try22-opt-scwrl.pdb CostConform Time quit