// To be run from pce/casp5/t0174 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ //ConformFromSeq replace // get a random conformation, removing all-zero one //NameConform T0174.rand //Time InFilePrefix ReadTemplateAtoms Template.atoms //Include T0174.t2k.undertaker-align.script //ReadFragmentAlignment T0174.t2k-2track-undertaker.a2m //InfilePrefix 1gci/ // include read-alignments.under InfilePrefix Time // ReadConformPDB robetta1.pdb // NameConform T0174.try2-robetta1 // ReadConformPDB robetta2.pdb // NameConform T0174.try2-robetta2 // ReadConformPDB robetta3.pdb // NameConform T0174.try2-robetta3 // ReadConformPDB robetta4.pdb // NameConform T0174.try2-robetta4 // ReadConformPDB robetta5.pdb // NameConform T0174.try2-robetta5 ReadConformPDB decoys/T0174.try5-opt-scwrl.pdb NameConform T0174.try6-try5 ReportCost undertaker-try6.rdb TryAllAlign shrink 0.4 min_keep_length 5 TryAllAlign shrink 0.4 min_keep_length 5 cumulative NameConform T0174.try6-al2 PrintConformPDB T0174.try6-al2.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0174.try6-al4 PrintConformPDB T0174.try6-al4.pdb edges TryAllAlign shrink 0.3 min_keep_length 4 TryAllAlign shrink 0.3 min_keep_length 4 cumulative NameConform T0174.try6-al6 PrintConformPDB T0174.try6-al6.pdb edges TryAllAlign shrink 0.1 min_keep_length 2 TryAllAlign shrink 0.1 min_keep_length 2 cumulative NameConform T0174.try6-al8 PrintConformPDB T0174.try6-al8.pdb edges TryAllAlign shrink 0.2 min_keep_length 3 TryAllAlign shrink 0.2 min_keep_length 3 cumulative NameConform T0174.try6-al10 PrintConformPDB T0174.try6-al10.pdb edges TryAllAlign shrink 0. min_keep_length 1 TryAllAlign shrink 0. min_keep_length 1 cumulative NameConform T0174.try6-al12 PrintConformPDB T0174.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 T0174.t2k.frag InfilePrefix 1kkoA/ include read-alignments.under InfilePrefix 1k47A/ include read-alignments.under InfilePrefix 1jksA/ include read-alignments.under InfilePrefix 1eepB/ include read-alignments.under InfilePrefix 1qo7A/ include read-alignments.under InfilePrefix 174lA/ include read-alignments.under InfilePrefix 192l/ include read-alignments.under InfilePrefix 1l00/ include read-alignments.under InfilePrefix 1dk8A/ include read-alignments.under InfilePrefix 1hssA/ include read-alignments.under InfilePrefix t0174-1-200/1kkoA/ include read-alignments.under InfilePrefix t0174-1-200/1jksA/ include read-alignments.under InfilePrefix t0174-1-200/1l00/ include read-alignments.under InfilePrefix t0174-1-200/192l/ include read-alignments.under InfilePrefix t0174-1-200/1l92/ include read-alignments.under InfilePrefix t0174-1-200/174lA/ include read-alignments.under InfilePrefix t0174-1-200/1gjwA/ include read-alignments.under InfilePrefix t0174-1-200/1gjuA/ include read-alignments.under InfilePrefix t0174-1-200/1d3fA/ include read-alignments.under InfilePrefix t0174-1-200/224l/ include read-alignments.under InfilePrefix InfilePrefix t0174-101-300/1f3jB/ include read-alignments.under InfilePrefix t0174-101-300/1im5A/ include read-alignments.under InfilePrefix t0174-101-300/1es0B/ include read-alignments.under InfilePrefix t0174-101-300/2iadB/ include read-alignments.under InfilePrefix t0174-101-300/1iaoB/ include read-alignments.under InfilePrefix t0174-101-300/1bneC/ include read-alignments.under InfilePrefix t0174-101-300/1d9kD/ include read-alignments.under InfilePrefix t0174-101-300/1hlm/ include read-alignments.under InfilePrefix t0174-101-300/1ky3A/ include read-alignments.under InfilePrefix t0174-101-300/1b80A/ include read-alignments.under InfilePrefix InfilePrefix t0174-201-417/1fjgS/ include read-alignments.under InfilePrefix t0174-201-417/1jk3A/ include read-alignments.under InfilePrefix t0174-201-417/1bg3A/ include read-alignments.under InfilePrefix t0174-201-417/1qkfA/ include read-alignments.under InfilePrefix t0174-201-417/1f0tA/ include read-alignments.under InfilePrefix t0174-201-417/1eliA/ include read-alignments.under InfilePrefix t0174-201-417/1qbgA/ include read-alignments.under InfilePrefix t0174-201-417/1h69A/ include read-alignments.under InfilePrefix t0174-201-417/1zzzA/ include read-alignments.under InfilePrefix t0174-201-417/1fxkA/ include read-alignments.under // 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 0.01 \ InsertFragment 10 \ CrossAndInsert 1 \ TwoFragment 1 \ InsertSpecificFragment 5 \ ReduceBreak 5 \ CloseGap 0.1 \ ReduceClash 1 \ JiggleSubtree 0.03 \ OptSubtree 0.03 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0174.try6 OptConform pool_size 40 num_gen 50 gen_size 180 super_iter 15 \ use_all scwrl_each pdb NameConform T0174.try6-opt PrintConformPDB T0174.try6-opt.pdb edges SCWRLConform NameConform T0174.try6-opt-scwrl PrintConformPDB T0174.try6-opt-scwrl.pdb CostConform Time quit