// To be run from pce/casp5/t0191 // SetSeed 1031974050 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0191.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0191.t2k.undertaker-align.script ReadFragmentAlignment T0191.t2k-2track-undertaker.a2m InFilePrefix 1gpjA/ include read-alignments.under InFilePrefix 1ff9A/ include read-alignments.under InFilePrefix 1sayA/ include read-alignments.under InFilePrefix 1pjbA/ include read-alignments.under InFilePrefix 1jaxA/ include read-alignments.under InFilePrefix 1pjcA/ include read-alignments.under InFilePrefix 1d4fA/ include read-alignments.under InFilePrefix 1b3rA/ include read-alignments.under InFilePrefix 1a7aA/ include read-alignments.under InFilePrefix 1jayA/ include read-alignments.under InFilePrefix 1cydA/ include read-alignments.under InFilePrefix 1lehA/ include read-alignments.under InFilePrefix 1gegA/ include read-alignments.under InFilePrefix 1fmcA/ include read-alignments.under InFilePrefix 1gtmA/ include read-alignments.under InfilePrefix t0191-1-110/1gpjA/ include read-alignments.under InfilePrefix t0191-1-110/1dl5A/ include read-alignments.under InfilePrefix t0191-1-110/8abp/ include read-alignments.under InfilePrefix t0191-1-110/1ccwA/ include read-alignments.under InfilePrefix t0191-1-110/1qnf/ include read-alignments.under InfilePrefix t0191-1-110/1dxeA/ include read-alignments.under InfilePrefix t0191-1-110/1jr2A/ include read-alignments.under InfilePrefix t0191-1-110/1j97A/ include read-alignments.under InfilePrefix t0191-1-110/1f5sA/ include read-alignments.under InfilePrefix t0191-1-110/1a99A/ include read-alignments.under InfilePrefix t0191-101-260/1gpjA/ include read-alignments.under InfilePrefix t0191-101-260/1ff9A/ include read-alignments.under InfilePrefix t0191-101-260/1jaxA/ include read-alignments.under InfilePrefix t0191-101-260/1sayA/ include read-alignments.under InfilePrefix t0191-101-260/1pjbA/ include read-alignments.under InfilePrefix t0191-101-260/1fmcA/ include read-alignments.under InfilePrefix t0191-101-260/1gegA/ include read-alignments.under InfilePrefix t0191-101-260/1cydA/ include read-alignments.under InfilePrefix t0191-101-260/1pjcA/ include read-alignments.under InfilePrefix t0191-241-282/1gpjA/ include read-alignments.under InfilePrefix t0191-241-282/1ayyA/ include read-alignments.under InfilePrefix t0191-241-282/1jqsB/ include read-alignments.under InfilePrefix t0191-241-282/6xia/ include read-alignments.under InfilePrefix t0191-241-282/1qjhA/ include read-alignments.under InfilePrefix t0191-241-282/1dy1A/ include read-alignments.under InfilePrefix t0191-241-282/1eg0C/ include read-alignments.under InfilePrefix t0191-241-282/1g1xA/ include read-alignments.under InfilePrefix t0191-241-282/1jqsB/ include read-alignments.under InfilePrefix t0191-241-282/1bccF/ include read-alignments.under InfilePrefix // ReadConformPDB decoys/T0191.try5-opt.pdb // NameConform T0191.try6-try5 InfilePrefix decoys/ // ReadConformPDB T0191.try3.8.60.pdb // NameConform T0191.try9-try3-8 // ReadConformPDB T0191.try7-al2.pdb // NameConform T0191.try9-try7-al2 // ReadConformPDB T0191.try7.15.60.pdb // NameConform T0191.try9-try7-15 // ReadConformPDB T0191.try8-al2.pdb // NameConform T0191.try9-try8-al2 // ReadConformPDB T0191.try8-al4.pdb // NameConform T0191.try9-try8-al4 // ReadConformPDB T0191.try8-al6.pdb // NameConform T0191.try9-try8-al6 // ReadConformPDB T0191.try8-al6+1qnf-T0191-local-adpstyle5.pw.a2m.gz:1qnf.0.40.pdb // NameConform T0191.try9-try8.0 // ReadConformPDB T0191.try3.8.60.pdb // NameConform T0191.try10-try3-8 // ReadConformPDB T0191.try7-al2.pdb // NameConform T0191.try10-try7-al2 // ReadConformPDB T0191.try7.15.60.pdb // NameConform T0191.try10-try7-15 // ReadConformPDB T0191.try8-al6.pdb // NameConform T0191.try10-try8-al6 // ReadConformPDB T0191.try9-opt-scwrl.pdb // NameConform T0191.try10-try9 // ReadConformPDB T0191.try7.15.60.pdb // NameConform T0191.try11-try7-15 // ReadConformPDB T0191.try9-opt-scwrl.pdb // NameConform T0191.try11-try9 // ReadConformPDB T0191.try10-opt.pdb // NameConform T0191.try11-try10 // ReadConformPDB T0191.cut-moved.pdb // NameConform T0191.try13-cut // ReadConformPDB T0191.cut-moved2.pdb // NameConform T0191.try14-cut // ReadConformPDB T0191.cut-moved2.pdb // NameConform T0191.try15-cut ReadConformPDB T0191.try14-opt.pdb NameConform T0191.try16-try14 ReadConformPDB T0191.try15-opt.pdb NameConform T0191.try16-try15 ReadConformPDB T0191.try15.8.10.pdb NameConform T0191.try16-try15-8 ReadConformPDB T0191.try15.6.10.pdb NameConform T0191.try16-try15-6 InfilePrefix Time ReportCost undertaker-try16.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0191.try16-al2 // PrintConformPDB T0191.try16-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0191.try16-al4 // PrintConformPDB T0191.try16-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0191.try16-al6 // PrintConformPDB T0191.try16-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0191.try16-al8 // PrintConformPDB T0191.try16-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0191.try16-al10 // PrintConformPDB T0191.try16-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0191.try16-al12 // PrintConformPDB T0191.try16-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 T0191.t2k.frag ReadFragmentAlignment t0191-1-110/T0191.t2k.frag ReadFragmentAlignment t0191-101-260/T0191.t2k.frag ReadFragmentAlignment t0191-241-282/T0191.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 \ OneRotamer 0.03 \ ClashingRotamer 0.5 \ InsertFragment 5 \ CrossAndInsert 5 \ CrossOver 0 \ TwoFragment 10 \ InsertSpecificFragment 8 \ ReduceBreak 1 \ CloseGap 0.2 \ ReduceClash 5 \ ReduceConstraint 5 \ JiggleSubtree 0.03 \ OptSubtree 0.03 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0191.try16 OptConform pool_size 40 num_gen 200 gen_size 200 super_iter 1 \ pdb use_all no_initial_fill // scwrl_each NameConform T0191.try16-opt PrintConformPDB T0191.try16-opt.pdb edges SCWRLConform NameConform T0191.try16-opt-scwrl PrintConformPDB T0191.try16-opt-scwrl.pdb CostConform Time quit