// To be run from pce/casp5/t0195 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms Include T0195.t2k.undertaker-align.script ReadFragmentAlignment T0195.t2k-2track-undertaker.a2m InfilePrefix 1jjfA/ include read-alignments.under InfilePrefix 1dqyA/ include read-alignments.under InfilePrefix 1dqzA/ include read-alignments.under InfilePrefix 1f0nA/ include read-alignments.under InfilePrefix 1jt2A/ include read-alignments.under InfilePrefix 1gkkA/ include read-alignments.under InfilePrefix 1gklA/ include read-alignments.under InfilePrefix 1jfrA/ include read-alignments.under InfilePrefix 1fj2A/ include read-alignments.under InfilePrefix 1jjiA/ include read-alignments.under InfilePrefix 1c4xA/ include read-alignments.under InfilePrefix 1aurA/ include read-alignments.under InfilePrefix 1auoA/ include read-alignments.under InfilePrefix 1qfmA/ include read-alignments.under InfilePrefix 1jkmA/ include read-alignments.under InfilePrefix 1jkmB/ include read-alignments.under InfilePrefix 1qe3A/ include read-alignments.under InfilePrefix 1hlgA/ include read-alignments.under InfilePrefix 1din/ include read-alignments.under InfilePrefix 1a8q/ include read-alignments.under InfilePrefix 1a88A/ include read-alignments.under InfilePrefix 1cr6B/ include read-alignments.under InfilePrefix 1a8s/ include read-alignments.under InfilePrefix 1ehyA/ include read-alignments.under InfilePrefix 2bce/ include read-alignments.under InfilePrefix 1cqzA/ include read-alignments.under InfilePrefix Time // ReadConformPDB decoys/T0195.try1-opt-scwrl.pdb // nameConform try3-try1 // ReadConformPDB decoys/T0195.try2.1.100.pdb // nameConform T0195.try4-try2-1 // ReadConformPDB decoys/T0195.try2.0.100.pdb // nameConform T0195.try4-try2-0 // ReadConformPDB decoys/T0195.try3-opt.pdb // nameConform T0195.try4-try3 // ReadConformPDB decoys/T0195.try2-opt.pdb // nameConform T0195.try5-try2 // ReadConformPDB decoys/T0195.try4-opt.pdb // nameConform T0195.try5-try4 // ReadConformPDB decoys/T0195.try2-opt.pdb // nameConform T0195.try6-try2 // ReadConformPDB decoys/T0195.try4-opt.pdb // nameConform T0195.try6-try4 // ReadConformPDB decoys/T0195.try5-opt.pdb // nameConform T0195.try6-try5 // ReadConformPDB decoys/T0195.try3.6.50.pdb // nameConform T0195.try7-try3-6 // ReadConformPDB decoys/T0195.try4-opt.pdb // nameConform T0195.try7-try4 // ReadConformPDB decoys/T0195.try2.0.100.pdb // nameConform T0195.try7-try2-0 // ReadConformPDB decoys/T0195.try1.12.60.pdb // nameConform T0195.try7-try1-12 // ReadConformPDB decoys/T0195.try6-opt.pdb // nameConform T0195.try7-try6 // ReadConformPDB decoys/T0195.try5-opt.pdb // nameConform T0195.try7-try5 //ReadConformPDB decoys/T0195.try2-opt.pdb // nameConform T0195.try8-try2 //ReadConformPDB decoys/T0195.try4-opt.pdb // nameConform T0195.try8-try4 //ReadConformPDB decoys/T0195.try6-opt.pdb // nameConform T0195.try8-try6 //ReadConformPDB decoys/T0195.try7-opt.pdb // nameConform T0195.try8-try7 //ReadConformPDB decoys/T0195.try5-opt.pdb // nameConform T0195.try8-try5 ReadConformPDB decoys/T0195.try4-opt.pdb nameConform T0195.try9-try4 ReadConformPDB decoys/T0195.try7-opt.pdb nameConform T0195.try9-try7 ReadConformPDB decoys/T0195.try6-opt.pdb nameConform T0195.try9-try6 ReadConformPDB decoys/T0195.try5-opt.pdb nameConform T0195.try9-try5 ReadConformPDB decoys/T0195.try8-opt.pdb nameConform T0195.try9-try8 ReportCost undertaker-try9.rdb // ConformFromSeq replace // get a random conformation, removing all-zero one // NameConform T0195.rand // Time // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0195.try9-al2 // PrintConformPDB T0195.try9-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0195.try9-al4 // PrintConformPDB T0195.try9-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0195.try9-al6 // PrintConformPDB T0195.try9-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0195.try9-al8 // PrintConformPDB T0195.try9-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0195.try9-al10 // PrintConformPDB T0195.try9-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0195.try9-al12 // PrintConformPDB T0195.try9-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 T0195.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 \ OneRotamer 0.01 \ ClashingRotamer 0.5 \ InsertFragment 10 \ CrossAndInsert 15 \ TwoFragment 20 \ InsertSpecificFragment 5 \ ReduceBreak 10 \ CloseGap 0.1 \ ReduceClash 1 \ ReduceConstraint 5 \ JiggleSubtree 0.02 \ OptSubtree 0.01 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0195.try9 OptConform pool_size 40 num_gen 150 gen_size 160 super_iter 1 \ pdb use_all // scwrl_each NameConform T0195.try9-opt PrintConformPDB T0195.try9-opt.pdb edges // SCWRLConform // NameConform T0195.try9-opt-scwrl // PrintConformPDB T0195.try9-opt-scwrl.pdb CostConform Time quit