// To be run from pce/casp5/t0136 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms ReadFragmentAlignment T0136-1hzdA.vast.a2m ReadFragmentAlignment T0136-bob.vast.a2m ReadFragmentAlignment T0136-1nzyA.vast-hand.a2m Include T0136.undertaker-align.script ReadFragmentAlignment T0136.t2k-2track-undertaker.a2m // ConformFromSeq replace // get a random conformation, removing all-zero one // NameConform T0136.rand ReadConformPDB decoys/T0136.try15-opt-scwrl.pdb NameConform T0136.try17-try15 TryAllAlign shrink 0.3 min_keep_length 1 NameConfor m0136.try17-al1 TryAllAlign shrink 0.1 min_keep_length 1 NameConfor m0136.try17-al2 TryAllAlign shrink 0 min_keep_length 1 NameConfor m0136.try17-al3 TryAllAlign shrink 0.3 min_keep_length 1 NameConfor m0136.try17-al4 TryAllAlign shrink 0.1 min_keep_length 1 NameConfor m0136.try17-al5 TryAllAlign shrink 0 min_keep_length 1 NameConfor m0136.try17-al6 ReadConformPDB decoys/T0136.try7-opt-scwrl.pdb NameConform T0136.try17-try7 InFilePrefix t0136-1-80/1ivhA/ include read-alignments.under InFilePrefix t0136-1-80/1fuoA/ include read-alignments.under InFilePrefix t0136-1-80/1furA/ include read-alignments.under InFilePrefix t0136-1-80/1bpoA/ include read-alignments.under InFilePrefix t0136-1-80/1a5lC/ include read-alignments.under InFilePrefix t0136-1-80/1a5oC/ include read-alignments.under InFilePrefix t0136-1-80/1ejsC/ include read-alignments.under InFilePrefix t0136-1-80/2pbg/ include read-alignments.under InFilePrefix t0136-1-80/1fwgC/ include read-alignments.under InFilePrefix t0136-1-80/1krbC/ include read-alignments.under # 1-290 InfilePrefix t0136-1-290/1dciA/ include read-alignments.under InfilePrefix t0136-1-290/1ef8A/ include read-alignments.under InfilePrefix t0136-1-290/1hnuA/ include read-alignments.under InfilePrefix t0136-1-290/1hnoA/ include read-alignments.under InfilePrefix t0136-1-290/1hzdA/ include read-alignments.under InfilePrefix t0136-1-290/2dubE/ include read-alignments.under InfilePrefix t0136-1-290/1nzyA/ include read-alignments.under # 80-290 InfilePrefix t0136-80-290/1dciA/ include read-alignments.under InfilePrefix t0136-80-290/1ef8A/ include read-alignments.under InfilePrefix t0136-80-290/1hnuA/ include read-alignments.under InfilePrefix t0136-80-290/1hnoA/ include read-alignments.under InfilePrefix t0136-80-290/1hzdA/ include read-alignments.under InfilePrefix t0136-80-290/2dubE/ include read-alignments.under InfilePrefix t0136-80-290/1nzyA/ include read-alignments.under # 250-523 InfilePrefix t0136-250-523/1dciA/ include read-alignments.under InfilePrefix t0136-250-523/1ef8A/ include read-alignments.under InfilePrefix t0136-250-523/1hnuA/ include read-alignments.under InfilePrefix t0136-250-523/1hnoA/ include read-alignments.under InfilePrefix t0136-250-523/1hzdA/ include read-alignments.under InfilePrefix t0136-250-523/2dubE/ include read-alignments.under InfilePrefix t0136-250-523/1nzyA/ include read-alignments.under InFilePrefix // ReadConformPDB decoys/T0136.try2-opt.pdb // NameConform T0136.try2-try3 // ReadConformPDB decoys/T0136.try4.17.60.pdb // NameConform T0136.try5-try4 // ReadConformPDB decoys/T0136.try5-opt.pdb // NameConform T0136.try6-try5 // ReadConformPDB decoys/T0136.try5-opt-scwrl.pdb // NameConform T0136.try6-try5-s // ReadConformPDB decoys/T0136.cut-and-paste1.pdb // NameConform T0136.try7-cut // ReadConformPDB decoys/T0136.try7-opt-scwrl.pdb // NameConform T0136.try8-try7 // ReadConformPDB decoys/T0136.cut-and-paste2.pdb // NameConform T0136.try9-cut // ReadConformPDB decoys/T0136.try9-opt.pdb // NameConform T0136.try10-try9 // ReadConformPDB decoys/T0136-moved3.pdb // NameConform T0136.try11 // ReadConformPDB decoys/T0136.try10-opt-scwrl.pdb // NameConform T0136.try13-try10 // ReadConformPDB decoys/T0136.try13-opt.pdb // NameConform T0136.try14-try13 // ReadConformPDB decoys/T0136.try8-opt-scwrl.pdb // NameConform T0136.try14-try8 // ReadConformPDB decoys/T0136.try7.4.40.pdb // NameConform T0136.try14-try7-4 // ReadConformPDB decoys/T0136.try6-opt-scwrl.pdb // NameConform T0136.try14-try6 // ReadConformPDB decoys/T0136.try14-opt.pdb // NameConform T0136.try15-try14 // ReadConformPDB decoys/T0136.try8.2.50.pdb // NameConform T0136.try15-try8-2 // ReadConformPDB decoys/T0136.try7-opt.pdb // NameConform T0136.try15-try7 // ReadConformPDB decoys/T0136.try6-opt-scwrl.pdb // NameConform T0136.try15-try6 // ReadConformPDB decoys/T0136.try9.2.50.pdb // NameConform T0136.try15-try9-2 // ReadConformPDB decoys/T0136.try5-al10-scwrl.10.50.pdb // NameConform T0136.try15-try5-10 // ReadConformPDB decoys/T0136.try4.17.60.pdb // NameConform T0136.try15-try4-17 // ReadConformPDB decoys/T0136.try13.2.50.pdb // NameConform T0136.try15-try13-2 // ReadConformPDB decoys/T0136.try11.19.15.pdb // NameConform T0136.try15-try11-19 // ReadConformPDB decoys/T0136.try12.18.15.pdb // NameConform T0136.try15-try12-18 // ReadConformPDB decoys/T0136.try10.3.50.pdb // NameConform T0136.try15-try10-3 // ReadConformPDB decoys/T0136-try1-opt.pdb // NameConform T0136.try15-try1 Time ReportCost undertaker-try17.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0136.try17-al2 // PrintConformPDB T0136.try17-al2.pdb edges // // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0136.try17-al4 // PrintConformPDB T0136.try17-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0136.try17-al6 // PrintConformPDB T0136.try17-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0136.try17-al8 // PrintConformPDB T0136.try17-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0136.try17-al10 // PrintConformPDB T0136.try17-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0136.try17-al12 // PrintConformPDB T0136.try17-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 T0136.t2k.frag OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0 \ ClashingRotamer 1 \ OneRotamer 0.1 \ InsertFragment 3 \ CrossAndInsert 4 \ CrossOver 0 \ TwoFragment 2 \ InsertSpecificFragment 6 \ ReduceBreak 2 \ CloseGap 0.1 \ ReduceClash 1 \ ReduceConstraint 0.3 \ JiggleSubTree 0.06 \ OptSubtree 0.05 \ ImproveSSBond 0 \ InsertSSBond 0 NameConform T0136.try17 OptConform pool_size 40 num_gen 100 gen_size 100 super_iter 2 \ use_all pdb // scwrl_each NameConform T0136.try17-opt PrintConformPDB T0136.try17-opt.pdb edges SCWRLConform NameConform T0136.try17-opt-scwrl PrintConformPDB T0136.try17-opt-scwrl.pdb CostConform Time quit // ordinary optimization: // InitMethodProbs InsertAlignment 0.1 \ // ClashingRotamer 0.5 \ // InsertFragment 11 \ // CrossAndInsert 1 \ // OneRotamer 0.01 \ // CrossOver 0 \ // TwoFragment 1 \ // InsertSpecificFragment 5 \ // ReduceBreak 2 \ // CloseGap 0.1 \ // ReduceClash 1 \ // JiggleSubTree 0.03 \ // OptSubtree 0.03 \ // InsertSSBond 0 // // NameConform T0136.try17 // OptConform pool_size 40 num_gen 50 gen_size 100 super_iter 5 \ // scwrl_each use_all pdb // Fix up moved pieces: // InitMethodProbs InsertAlignment 0.1 \ // ClashingRotamer 0.5 \ // InsertFragment 11 \ // CrossAndInsert 1 \ // OneRotamer 0.01 \ // CrossOver 0 \ // TwoFragment 1 \ // InsertSpecificFragment 5 \ // ReduceBreak 2 \ // CloseGap 0.1 \ // ReduceClash 1 \ // JiggleSubTree 0.03 \ // OptSubtree 1 \ // InsertSSBond 0 // NameConform T0136.try17 // OptConform pool_size 40 num_gen 15 gen_size 200 super_iter 20 \ scwrl_each use_all pdb no_initial_fill