// To be run from pce/casp5/t0194 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0194.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0194.t2k.undertaker-align.script ReadFragmentAlignment T0194.t2k-2track-undertaker.a2m InFilePrefix 1d2nA/ include read-alignments.under //InFilePrefix 1bdg/ // include read-alignments.under //InFilePrefix 1opy/ // include read-alignments.under //InFilePrefix 1heuA/ // include read-alignments.under //InFilePrefix 1ee2A/ // include read-alignments.under //InFilePrefix 1hetA/ // include read-alignments.under //InFilePrefix 1qi6A/ // include read-alignments.under //InFilePrefix 1euhA/ // include read-alignments.under //InFilePrefix 1xze/ // include read-alignments.under //InFilePrefix 1d2nA/ // include read-alignments.under //InFilePrefix 9gacA/ // include read-alignments.under //InFilePrefix 2pgd/ // include read-alignments.under //InFilePrefix 1e32A/ // include read-alignments.under //InFilePrefix 1g6oA/ // include read-alignments.under //InFilePrefix 1jbkA/ // include read-alignments.under //InFilePrefix 1d2mA/ // include read-alignments.under InfilePrefix // ReadConformPDB decoys/T0194.try2-opt-scwrl.pdb // NameConform T0186.try6-try2 // ReadConformPDB decoys/T0194.try3-opt-scwrl.pdb // NameConform T0186.try6-try3 // ReadConformPDB decoys/T0194.try5-opt-scwrl.pdb // NameConform T0186.try6-try3 // ReadConformPDB decoys/T0194.try5-opt-scwrl.pdb // NameConform T0186.try8-try5 // ReadConformPDB decoys/T0194.try6.0.60.pdb // NameConform T0186.try8-try6-0 // ReadConformPDB decoys/T0194.try6.1.60.pdb // NameConform T0186.try8-try6-1 //ReadConformPDB decoys/T0194.try5-opt-scwrl.pdb // NameConform T0186.try12-try5 //ReadConformPDB decoys/T0194.try6.0.60.pdb // NameConform T0186.try12-try6-0 //ReadConformPDB decoys/T0194.try6.1.60.pdb // NameConform T0186.try12-try6-1 Time ReportCost undertaker-try12.rdb TryAllAlign shrink 0.4 min_keep_length 5 TryAllAlign shrink 0.4 min_keep_length 5 cumulative NameConform T0194.try12-al2 PrintConformPDB T0194.try12-al2.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0194.try12-al4 PrintConformPDB T0194.try12-al4.pdb edges TryAllAlign shrink 0.3 min_keep_length 4 TryAllAlign shrink 0.3 min_keep_length 4 cumulative NameConform T0194.try12-al6 PrintConformPDB T0194.try12-al6.pdb edges TryAllAlign shrink 0.1 min_keep_length 2 TryAllAlign shrink 0.1 min_keep_length 2 cumulative NameConform T0194.try12-al8 PrintConformPDB T0194.try12-al8.pdb edges TryAllAlign shrink 0.2 min_keep_length 3 TryAllAlign shrink 0.2 min_keep_length 3 cumulative NameConform T0194.try12-al10 PrintConformPDB T0194.try12-al10.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0194.try12-al12 PrintConformPDB T0194.try12-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 T0194.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 0.02 \ InsertFragment 10 \ CrossAndInsert 10 \ CrossOver 0 \ TwoFragment 10 \ InsertSpecificFragment 10 \ ReduceBreak 5 \ CloseGap 0.1 \ ReduceClash 1 \ ReduceConstraint 1 \ JiggleSubtree 0.03 \ OptSubtree 0.03 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0194.try12 OptConform pool_size 40 num_gen 100 gen_size 180 super_iter 5 \ use_all pdb NameConform T0194.try12-opt PrintConformPDB T0194.try12-opt.pdb edges // SCWRLConform // NameConform T0194.try12-opt-scwrl // PrintConformPDB T0194.try12-opt-scwrl.pdb CostConform Time quit