// To be run from pce/casp5/t0182 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0182.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0182.t2k.undertaker-align.script ReadFragmentAlignment T0182.t2k-2track-undertaker.a2m InfilePrefix 1c24A/ include read-alignments.under InfilePrefix 1mat/ include read-alignments.under InfilePrefix 2matA/ include read-alignments.under InfilePrefix 1a16/ include read-alignments.under InfilePrefix 1az9/ include read-alignments.under InfilePrefix 1xgsA/ include read-alignments.under InfilePrefix 1b6a/ include read-alignments.under InfilePrefix 1chmA/ include read-alignments.under InfilePrefix 1bn5/ include read-alignments.under InfilePrefix 3matA/ include read-alignments.under InfilePrefix 4matA/ include read-alignments.under InfilePrefix Time // ReadConformPDB decoys/T0182.try1.9.60.pdb // NameConform T0182.try2-try1-9 // ReadConformPDB decoys/T0182.try1-opt-scwrl.pdb // NameConform T0182.try2-try1 // ReadConformPDB decoys/T0182.try1.15.60.pdb // NameConform T0182.try2-try1-15 // ReadConformPDB decoys/T0182.try1.13.60.pdb // NameConform T0182.try2-try1-13 // ReadConformPDB decoys/T0182.try1.9.60.pdb // NameConform T0182.try3-try1-9 // ReadConformPDB decoys/T0182.try1-opt-scwrl.pdb // NameConform T0182.try3-try1 // ReadConformPDB decoys/T0182.try1.15.60.pdb // NameConform T0182.try3-try1-15 // ReadConformPDB decoys/T0182.try1.13.60.pdb // NameConform T0182.try3-try1-13 // ReadConformPDB decoys/T0182.try1.9.60.pdb // NameConform T0182.try4-try1-9 // ReadConformPDB decoys/T0182.try1-opt-scwrl.pdb // NameConform T0182.try4-try1 // ReadConformPDB decoys/T0182.try1.15.60.pdb // NameConform T0182.try4-try1-15 // ReadConformPDB decoys/T0182.try1.13.60.pdb // NameConform T0182.try4-try1-13 // ReadConformPDB decoys/T0182.try2.0.120.pdb // NameConform T0182.try4-try2-0 // ReadConformPDB decoys/T0182.try2.1.120.pdb // NameConform T0182.try4-try2-1 // ReadConformPDB decoys/T0182.try3.0.120.pdb // NameConform T0182.try4-try3-0 // ReadConformPDB decoys/T0182.try3.1.120.pdb // NameConform T0182.try4-try3-1 // ReadConformPDB decoys/T0182.try1.9.60.pdb // NameConform T0182.try5-try1-9 // ReadConformPDB decoys/T0182.try1-opt-scwrl.pdb // NameConform T0182.try5-try1 // ReadConformPDB decoys/T0182.try1.15.60.pdb // NameConform T0182.try5-try1-15 // ReadConformPDB decoys/T0182.try1.13.60.pdb // NameConform T0182.try5-try1-13 // ReadConformPDB decoys/T0182.try2.0.120.pdb // NameConform T0182.try5-try2-0 // ReadConformPDB decoys/T0182.try2.1.120.pdb // NameConform T0182.try5-try2-1 // ReadConformPDB decoys/T0182.try3.0.120.pdb // NameConform T0182.try5-try3-0 // ReadConformPDB decoys/T0182.try3.1.120.pdb // NameConform T0182.try5-try3-1 ReadConformPDB decoys/T0182.try4.3.120.pdb NameConform T0182.try6-try4-3 ReadConformPDB decoys/T0182.try4.4.120.pdb NameConform T0182.try6-try4-4 ReadConformPDB decoys/T0182.try4.9.120.pdb NameConform T0182.try6-try4-9 ReadConformPDB decoys/T0182.try4.8.120.pdb NameConform T0182.try6-try4-8 ReadConformPDB decoys/T0182.try4.2.120.pdb NameConform T0182.try6-try4-2 ReadConformPDB decoys/T0182.try4.5.120.pdb NameConform T0182.try6-try4-5 ReadConformPDB decoys/T0182.try4-opt.pdb NameConform T0182.try6-try4 ReportCost undertaker-try6.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0182.try6-al2 // PrintConformPDB T0182.try6-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0182.try6-al4 // PrintConformPDB T0182.try6-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0182.try6-al6 // PrintConformPDB T0182.try6-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0182.try6-al8 // PrintConformPDB T0182.try6-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0182.try6-al10 // PrintConformPDB T0182.try6-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0182.try6-al12 // PrintConformPDB T0182.try6-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 T0182.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 0.3 \ ClashingRotamer 0.5 \ OneRotamer 0.2 \ InsertFragment 5 \ CrossAndInsert 5 \ CrossOver 0 \ TwoFragment 1 \ InsertSpecificFragment 5 \ ReduceBreak 5 \ CloseGap 0.3 \ ReduceClash 1 \ JiggleSubtree 0.02 \ OptSubtree 0.03 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0182.try6 OptConform pool_size 40 num_gen 150 gen_size 180 super_iter 4 \ pdb use_all scwrl_each NameConform T0182.try6-opt PrintConformPDB T0182.try6-opt.pdb edges SCWRLConform NameConform T0182.try6-opt-scwrl PrintConformPDB T0182.try6-opt-scwrl.pdb CostConform Time quit