// To be run from pce/casp5/t0189 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0189.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0189.t2k.undertaker-align.script ReadFragmentAlignment T0189.t2k-2track-undertaker.a2m InfilePrefix 1rkd/ include read-alignments.under InfilePrefix 1bx4A/ include read-alignments.under InfilePrefix 1liiA/ include read-alignments.under InfilePrefix 1lioA/ include read-alignments.under InfilePrefix 1dgmA/ include read-alignments.under InfilePrefix 1jxhA/ include read-alignments.under InfilePrefix 1c3qA/ include read-alignments.under InfilePrefix 1gc5A/ include read-alignments.under InfilePrefix 1ekqA/ include read-alignments.under InfilePrefix Time // ReadConformPdb decoys/T0189.try1-opt-scwrl.pdb // NameConform T0189.try2-try1 // ReadConformPdb decoys/T0189.try1-opt-scwrl.pdb // NameConform T0189.try4-try1 // ReadConformPdb decoys/T0189.try2-opt.pdb // NameConform T0189.try4-try2 // ReadConformPdb decoys/T0189.try3-opt.pdb // NameConform T0189.try4-try3 // ReadConformPdb decoys/T0189.try2-opt.pdb // NameConform T0189.try5-try2 // ReadConformPdb decoys/T0189.try3-opt.pdb // NameConform T0189.try5-try3 // ReadConformPdb decoys/T0189.try3.1.100.pdb // NameConform T0189.try5-try3-1 // ReadConformPdb decoys/T0189.try3.2.100.pdb // NameConform T0189.try5-try3-2 // ReadConformPdb decoys/T0189.try4.1.100.pdb // NameConform T0189.try5-try4-1 // ReadConformPdb decoys/T0189.try4.0.100.pdb // NameConform T0189.try5-try4-0 ReadConformPdb decoys/T0189.try2-opt.pdb NameConform T0189.try6-try2 ReadConformPdb decoys/T0189.try3-opt.pdb NameConform T0189.try6-try3 ReadConformPdb decoys/T0189.try4.1.100.pdb NameConform T0189.try6-try4-1 ReadConformPdb decoys/T0189.try4.0.100.pdb NameConform T0189.try6-try4-0 ReadConformPdb decoys/T0189.try5-opt.pdb NameConform T0189.try6-try5 ReportCost undertaker-try6.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0189.try6-al2 // PrintConformPDB T0189.try6-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0189.try6-al4 // PrintConformPDB T0189.try6-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0189.try6-al6 // PrintConformPDB T0189.try6-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0189.try6-al8 // PrintConformPDB T0189.try6-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0189.try6-al10 // PrintConformPDB T0189.try6-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0189.try6-al12 // PrintConformPDB T0189.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 T0189.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 \ OneRotamer 0.03 \ ClashingRotamer 1 \ InsertFragment 10 \ CrossAndInsert 5 \ TwoFragment 10 \ InsertSpecificFragment 5 \ ReduceBreak 10 \ CloseGap 0.2 \ ReduceClash 2 \ ReduceConstraint 5 \ JiggleSubtree 0.02 \ OptSubtree 0.02 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0189.try6 OptConform pool_size 40 num_gen 250 gen_size 180 super_iter 1 \ pdb use_all // scwrl_each NameConform T0189.try6-opt PrintConformPDB T0189.try6-opt.pdb edges SCWRLConform NameConform T0189.try6-opt-scwrl PrintConformPDB T0189.try6-opt-scwrl.pdb CostConform Time quit