// To be run from pce/casp5/t0151 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0151.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0151.t2k.undertaker-align.script ReadFragmentAlignment T0151.t2k-2track-undertaker.a2m Time ReportCost undertaker-try3.rdb ReadConformPdb decoys/T0151.try2-opt.pdb NameConform T0151.try3-try2 TryAllAlign shrink 0.4 min_keep_length 5 TryAllAlign shrink 0.4 min_keep_length 5 cumulative NameConform T0151.al2 PrintConformPDB T0151.try3-al2.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0151.try3-al4 PrintConformPDB T0151.try3-al4.pdb edges TryAllAlign shrink 0.3 min_keep_length 4 TryAllAlign shrink 0.3 min_keep_length 4 cumulative NameConform T0151.try3-al6 PrintConformPDB T0151.try3-al6.pdb edges TryAllAlign shrink 0.1 min_keep_length 2 TryAllAlign shrink 0.1 min_keep_length 2 cumulative NameConform T0151.try3-al8 PrintConformPDB T0151.try3-al8.pdb edges TryAllAlign shrink 0.2 min_keep_length 3 TryAllAlign shrink 0.2 min_keep_length 3 cumulative NameConform T0151.try3-al10 PrintConformPDB T0151.try3-al10.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0151.try3-al12 PrintConformPDB T0151.try3-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 T0151.t2k.frag OutFilePrefix PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs InsertAlignment 0.1 \ ClashingRotamer 0.5 \ InsertFragment 1 \ CrossAndInsert 1 \ TwoFragment 1 \ InsertSpecificFragment 0.5 \ ReduceBreak 5 \ CloseGap 0.01 \ ReduceClash 1 \ InsertSSBond 0 NameConform T0151.try3 OptConform pool_size 40 num_gen 20 gen_size 120 super_iter 20 \ pdb use_all scwrl_each NameConform T0151.try3-opt PrintConformPDB T0151.try3-opt.pdb edges SCWRLConform NameConform T0151.try3-opt-scwrl PrintConformPDB T0151.try3-opt-scwrl.pdb CostConform Time quit