// To be run from pce/casp5/t0183 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0183.rand Time InFilePrefix ReadTemplateAtoms Template.atoms ReadFragmentAlignment T0183-1jclA.vast-hand2.a2m // include try-alignments.under Time // ReadConformPDB decoys/T0183.try2.0.120.pdb // NameConform T0183.try4-try2-0 // ReadConformPDB decoys/T0183.try1.14.60.pdb // NameConform T0183.try4-try1-14 // ReadConformPDB decoys/T0183.try1.1.60.pdb // NameConform T0183.try4-try1-1 // ReadConformPDB decoys/T0183.try1.17.60.pdb // NameConform T0183.try4-try1-17 // ReadConformPDB decoys/T0183.try1.15.60.pdb // NameConform T0183.try4-try1-15 // ReadConformPDB decoys/T0183.try1.6.60.pdb // NameConform T0183.try4-try1-6 // ReadConformPDB decoys/T0183.try1.2.60.pdb // NameConform T0183.try5/-try1-2 // ReadConformPDB decoys/T0183.try1.16.60.pdb // NameConform T0183.try5-try1-16 // ReadConformPDB decoys/T0183.try1.19.60.pdb // NameConform T0183.try5-try1-19 // ReadConformPDB decoys/T0183.try1.2.60.pdb // NameConform T0183.try5-try1-2 // ReadConformPDB decoys/T0183.try1-opt.pdb // NameConform T0183.try5-try1 // ReadConformPDB decoys/T0183.try2.0.120.pdb // NameConform T0183.try5-try2-0 // ReadConformPDB decoys/T0183.try4-opt.pdb // NameConform T0183.try7-try4 // ReadConformPDB decoys/T0183.try3-opt.pdb // NameConform T0183.try7-try3 // ReadConformPDB decoys/T0183.try2-al12.pdb // NameConform T0183.try7-try2-al12 // ReadConformPDB decoys/T0183.try5-al4.3.120.pdb // NameConform T0183.try7-try5-3 // ReadConformPDB decoys/T0183.try5-al2.0.120.pdb // NameConform T0183.try7-try5-0 // ReadConformPDB decoys/T0183.try5-al8.1.120.pdb // NameConform T0183.try7-try5-1 // ReadConformPDB decoys/T0183.try5-al10.4.120.pdb // NameConform T0183.try7-try5-4 // ReadConformPDB decoys/T0183.try3-opt.pdb // NameConform T0183.try8-try3 // ReadConformPDB decoys/T0183.try3-al8.7.120.pdb // NameConform T0183.try8-try3-7 // ReadConformPDB decoys/T0183.try4-try2-0.5.120.pdb // NameConform T0183.try8-try4-5 // ReadConformPDB decoys/T0183.try7.4.120.pdb // NameConform T0183.try8-try7-4 // ReadConformPDB decoys/T0183.try5-al4.3.120.pdb // NameConform T0183.try8-try5-3 // ReadConformPDB decoys/T0183.try6-al10.0.60.pdb // NameConform T0183.try8-try6-0 // ReadConformPDB decoys/T0183.try6-al10.1.60.pdb // NameConform T0183.try8-try6-1 // ReadConformPDB decoys/T0183.try7.4.120.pdb // NameConform T0183.try9-try7-4 // ReadConformPDB decoys/T0183.try6-al10.1.60.pdb // NameConform T0183.try9-try6-1 // ReadConformPDB decoys/T0183.try8-opt.pdb // NameConform T0183.try9-try8 // ReadConformPDB decoys/T0183.try8-opt.pdb // NameConform T0183.try10-try8 // ReadConformPDB decoys/T0183.try9-opt.pdb // NameConform T0183.try10-try9 // ReadConformPDB decoys/T0183.try9-opt.pdb // NameConform T0183.try11-try9 // ReadConformPDB decoys/T0183.try10-opt.pdb // NameConform T0183.try11-try10 // ReadConformPDB decoys/T0183.try10-opt.pdb // NameConform T0183.try12-try10 // ReadConformPDB decoys/T0183.try11-opt.pdb // NameConform T0183.try12-try11 // ReadConformPDB decoys/T0183.try10-opt.pdb // NameConform T0183.try13-try10 // ReadConformPDB decoys/T0183.try11-opt.pdb // NameConform T0183.try13-try11 // ReadConformPDB decoys/T0183.try11-opt.pdb // NameConform T0183.try14-try11 // ReadConformPDB decoys/T0183.try12-opt.pdb // NameConform T0183.try14-try12 // ReadConformPDB decoys/T0183.try13-opt.pdb // NameConform T0183.try14-try13 // ReadConformPDB decoys/T0183.try12-opt.pdb // NameConform T0183.try15-try12 // ReadConformPDB decoys/T0183.try13-opt.pdb // NameConform T0183.try15-try13 // ReadConformPDB decoys/T0183.try14-opt.pdb // NameConform T0183.try15-try14 ReadConformPDB decoys/T0183.try17-opt.pdb NameConform T0183.try18-try17 ReportCost undertaker-try18.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0183.try18-al2 // PrintConformPDB T0183.try18-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0183.try18-al4 // PrintConformPDB T0183.try18-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0183.try18-al6 // PrintConformPDB T0183.try18-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0183.try18-al8 // PrintConformPDB T0183.try18-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0183.try18-al10 // PrintConformPDB T0183.try18-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0183.try18-al12 // PrintConformPDB T0183.try18-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 include try-alignments.under ReadFragmentAlignment T0183-1jclA.vast-hand.a2m ReadFragmentAlignment T0183.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 \ OneRotamer 0.05 \ InsertFragment 10 \ CrossOver 0 \ CrossAndInsert 10 \ TwoFragment 20 \ InsertSpecificFragment 10 \ ReduceBreak 3 \ CloseGap 0.5 \ ReduceClash 1 \ ReduceConstraint 1 \ JiggleSubtree 0.03 \ OptSubtree 0.03 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0183.try18 OptConform pool_size 40 num_gen 150 gen_size 200 super_iter 1 \ use_all pdb // scwrl_each NameConform T0183.try18-opt PrintConformPDB T0183.try18-opt.pdb edges SCWRLConform NameConform T0183.try18-opt-scwrl PrintConformPDB T0183.try18-opt-scwrl.pdb CostConform Time quit