// To be run from pce/casp5/t0193 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0193.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0193.t2k.undertaker-align.script ReadFragmentAlignment T0193.t2k-2track-undertaker.a2m // best-scoring templates InFilePrefix 1j5pA/ include read-alignments.under InFilePrefix 3dapA/ include read-alignments.under InFilePrefix 1dapA/ include read-alignments.under InFilePrefix 1f06A/ include read-alignments.under InFilePrefix 1gcuA/ include read-alignments.under InFilePrefix 1cf2O/ include read-alignments.under InFilePrefix 1lc0A/ include read-alignments.under InFilePrefix 1eudA/ include read-alignments.under InFilePrefix 1b7gO/ include read-alignments.under InFilePrefix 2scuA/ include read-alignments.under // possibly trashy templates, with forced alignments // selected because they had a domain that matched one of our predictions // for the c-terminal domain of the target, and had an earlier domain that // may allow us to extend the match earlier. // All of these alignments scored very badly, and were not introduced // until try7. InfilePrefix 1ejjA/ include read-alignments.under InfilePrefix 1b3rA/ include read-alignments.under InfilePrefix 1ep2B/ include read-alignments.under InfilePrefix 1f0kA/ include read-alignments.under InfilePrefix 2ohxA/ include read-alignments.under InfilePrefix 1lnqA/ include read-alignments.under InfilePrefix Time InfilePrefix decoys/ // ReadConformPDB T0193.try1-opt.pdb // NameConform T0193.try5-try1 // ReadConformPDB T0193.try2-opt.pdb // NameConform T0193.try5-try2 // ReadConformPDB T0193.try3-opt.pdb // NameConform T0193.try5-try3 // ReadConformPDB T0193.try4-opt.pdb // NameConform T0193.try5-try4 // ReadConformPDB T0193.try1-opt.pdb // NameConform T0193.try6-try1 // ReadConformPDB T0193.try2-opt.pdb // NameConform T0193.try6-try2 // ReadConformPDB T0193.try3-opt.pdb // NameConform T0193.try6-try3 // ReadConformPDB T0193.try4-opt.pdb // NameConform T0193.try6-try4 // ReadConformPDB T0193.try5-opt.pdb // NameConform T0193.try6-try5 // ReadConformPDB T0193.try5-opt.pdb // NameConform T0193.try9-try5 // ReadConformPDB T0193.try7-opt.pdb // NameConform T0193.try9-try7 // ReadConformPDB T0193.try8-opt.pdb // NameConform T0193.try9-try8 // ReadConformPDB T0193.try6-opt.pdb // NameConform T0193.try9-try6 // ReadConformPDB T0193.try3-opt.pdb // NameConform T0193.try10-try3 // ReadConformPDB T0193.try6-opt.pdb // NameConform T0193.try10-try6 // ReadConformPDB T0193.try8-opt.pdb // NameConform T0193.try10-try8 // ReadConformPDB T0193.try7-opt-scwrl.pdb // NameConform T0193.try10-try7-s // ReadConformPDB T0193.try9-opt.pdb // NameConform T0193.try10-try9 // readConformPDB T0193.try2-opt.pdb // NameConform T0193.try12-try2 // readConformPDB T0193.try7-opt.pdb // NameConform T0193.try12-try7 // readConformPDB T0193.try11-opt.pdb // NameConform T0193.try12-try11 // readConformPDB T0193.try2-opt.pdb // NameConform T0193.try13-try2 // readConformPDB T0193.try7-opt.pdb // NameConform T0193.try13-try7 // readConformPDB T0193.try11-opt.pdb // NameConform T0193.try13-try11 // readConformPDB T0193.try12-opt.pdb // NameConform T0193.try13-try12 // readConformPDB T0193-moved.pdb // NameConform T0193.try14-cut // readConformPDB T0193-moved.pdb // NameConform T0193.try15-cut // readConformPDB T0193.try1.7.60.pdb // NameConform T0193.try16-try1-7 // readConformPDB T0193.try10.2.200.pdb // NameConform T0193.try16-try10-2 // readConformPDB T0193.try2-al8+T0193-1gcuA-2track-protein-EBGHTL-local-adpstyle5.pw.a2m.gz:1gcuA.3.100.pdb // NameConform T0193.try16-try2-3 // readConformPDB T0193.try15-opt.pdb // NameConform T0193.try16-try15 // readConformPDB T0193.try2-al8+T0193-1gcuA-2track-protein-EBGHTL-local-adpstyle5.pw.a2m.gz:1gcuA.3.100.pdb // NameConform T0193.try17-try2-3 // readConformPDB T0193.try15-opt.pdb // NameConform T0193.try17-try15 // readConformPDB T0193.try16-opt.pdb // NameConform T0193.try17-try16 // readConformPDB T0193.try15-opt.pdb // NameConform T0193.try18-try15 // readConformPDB T0193.try16-opt.pdb // NameConform T0193.try18-try16 // readConformPDB T0193.try17-opt.pdb // NameConform T0193.try18-try17 // readConformPDB T0193.try15-opt.pdb // NameConform T0193.try19-try15 // readConformPDB T0193.try16-opt.pdb // NameConform T0193.try19-try16 // readConformPDB T0193.try17-opt.pdb // NameConform T0193.try19-try17 // readConformPDB T0193.try15-opt.pdb // NameConform T0193.try20-try15 // readConformPDB T0193.try16-opt.pdb // NameConform T0193.try20-try16 // readConformPDB T0193.try17-opt.pdb // NameConform T0193.try20-try17 // readConformPDB T0193-rot.pdb // NameConform T0193.try21 // readConformPDB T0193-rot21.pdb // NameConform T0193.try22 readConformPDB T0193.try7-opt.pdb NameConform T0193.try23-7 InFilePrefix ReportCost undertaker-try23.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0193.try23-al2 // PrintConformPDB T0193.try23-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0193.try23-al4 // PrintConformPDB T0193.try23-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0193.try23-al6 // PrintConformPDB T0193.try23-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0193.try23-al8 // PrintConformPDB T0193.try23-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0193.try23-al10 // PrintConformPDB T0193.try23-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0193.try23-al12 // PrintConformPDB T0193.try23-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 T0193.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 0.1 \ ClashingRotamer 1 \ OneRotamer 0.05 \ InsertFragment 5 \ CrossAndInsert 10 \ CrossOver 0 \ TwoFragment 15 \ InsertSpecificFragment 10 \ ReduceBreak 1 \ CloseGap 0.3 \ ReduceClash 1 \ ReduceConstraint 1 \ JiggleSubtree 0.005 \ OptSubtree 0.025 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0193.try23 OptConform pool_size 40 num_gen 120 gen_size 180 super_iter 1 \ pdb use_all // scwrl_each NameConform T0193.try23-opt PrintConformPDB T0193.try23-opt.pdb edges // SCWRLConform // NameConform T0193.try23-opt-scwrl // PrintConformPDB T0193.try23-opt-scwrl.pdb CostConform Time quit