// To be run from pce/casp5/t0164 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0164.rand Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0164.t2k.undertaker-align.script ReadFragmentAlignment T0164.t2k-2track-undertaker.a2m InfilePrefix 1a4yA/ Include read-alignments.under InfilePrefix 2bnh/ Include read-alignments.under InfilePrefix 1yrgA/ Include read-alignments.under InfilePrefix 1k5dC/ Include read-alignments.under InfilePrefix 1fqvA/ Include read-alignments.under InfilePrefix 1fs2A/ Include read-alignments.under InfilePrefix 1d0bA/ Include read-alignments.under InfilePrefix 1h6tA/ Include read-alignments.under InfilePrefix Time InfilePrefix decoys/ // ReadConformPDB T0164.try1.0.20.pdb // nameConform T0164.try2-try1-0 // ReadConformPDB T0164.try1.10.20.pdb // nameConform T0164.try2-try1-10 // ReadConformPDB T0164.try1.11.20.pdb // nameConform T0164.try2-try1-11 // ReadConformPDB T0164.try1.12.20.pdb // nameConform T0164.try2-try1-12 // ReadConformPDB T0164.try1.13.20.pdb // nameConform T0164.try2-try1-13 // ReadConformPDB T0164.try1.14.20.pdb // nameConform T0164.try2-try1-14 // ReadConformPDB T0164.try1.15.20.pdb // nameConform T0164.try2-try1-15 // ReadConformPDB T0164.try1.16.20.pdb // nameConform T0164.try2-try1-16 // ReadConformPDB T0164.try1.17.20.pdb // nameConform T0164.try2-try1-17 // ReadConformPDB T0164.try1.18.20.pdb // nameConform T0164.try2-try1-18 // ReadConformPDB T0164.try1.19.20.pdb // nameConform T0164.try2-try1-19 // ReadConformPDB T0164.try1.20.20.pdb // nameConform T0164.try2-try1-20 // ReadConformPDB T0164.try1.2.20.pdb // nameConform T0164.try2-try1-2 // ReadConformPDB T0164.try1.3.20.pdb // nameConform T0164.try2-try1-3 // ReadConformPDB T0164.try1.4.20.pdb // nameConform T0164.try2-try1-4 // ReadConformPDB T0164.try1.5.20.pdb // nameConform T0164.try2-try1-5 // ReadConformPDB T0164.try1.6.20.pdb // nameConform T0164.try2-try1-6 // ReadConformPDB T0164.try1.7.20.pdb // nameConform T0164.try2-try1-7 // ReadConformPDB T0164.try1.8.20.pdb // nameConform T0164.try2-try1-8 // ReadConformPDB T0164.try1.9.20.pdb // nameConform T0164.try2-try1-9 // ReadConformPDB T0164.try1-al10.pdb // nameConform T0164.try2-try1-al10 // ReadConformPDB T0164.try1-al12.pdb // nameConform T0164.try2-try1-al12 // ReadConformPDB T0164.try1-al2.pdb // nameConform T0164.try2-try1-al2 // ReadConformPDB T0164.try1-al4.pdb // nameConform T0164.try2-try1-al4 // ReadConformPDB T0164.try1-al6.pdb // nameConform T0164.try2-try1-al6 // ReadConformPDB T0164.try1-al8.pdb // nameConform T0164.try2-try1-al8 // ReadConformPDB T0164.try1-opt.pdb // nameConform T0164.try2-try1 // ReadConformPDB T0164.try1-opt-scwrl.pdb // nameConform T0164.try2-try1-scwrl // ReadConformPDB T0164.try1+T0164-1yrgA-local-adpstyle1.pw.a2m.gz:1yrgA.1.20.pdb // nameConform T0164.try2-try1-1 // ReadConformPDB T0164.try2-opt-scwrl.pdb // NameConform T0164.try3-try2 // ReadConformPDB T0164.try3.7.40.pdb // NameConform T0164.try4-try3-7 // ReadConformPDB T0164.try3.14.40.pdb // NameConform T0164.try4-try3-14 // ReadConformPDB T0164.try3.10.40.pdb // NameConform T0164.try4-try3-10 // ReadConformPDB T0164.try3.11.40.pdb // NameConform T0164.try4-try3-11 ReadConformPDB T0164.try3.13.40.pdb NameConform T0164.try5-try3-13 ReadConformPDB T0164.try3.11.40.pdb NameConform T0164.try5-try3-11 ReadConformPDB T0164.try4-opt.pdb NameConform T0164.try5-try4 InfilePrefix ReportCost undertaker-try5.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0164.try5-al2 // PrintConformPDB T0164.try5-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0164.try5-al4 // PrintConformPDB T0164.try5-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0164.try5-al6 // PrintConformPDB T0164.try5-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0164.try5-al8 // PrintConformPDB T0164.try5-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0164.try5-al10 // PrintConformPDB T0164.try5-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0164.try5-al12 // PrintConformPDB T0164.try5-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 T0164.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 \ ClashingRotamer 1 \ OneRotamer 0.4 \ InsertFragment 8 \ CrossAndInsert 1 \ TwoFragment 1 \ InsertSpecificFragment 5 \ ReduceBreak 5 \ CloseGap 0.08 \ ReduceClash 1 \ JiggleSubtree 0.04 \ OptSubtree 0.04 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0164.try5 OptConform pool_size 40 num_gen 90 gen_size 150 super_iter 6 \ pdb scwrl_each use_all NameConform T0164.try5-opt PrintConformPDB T0164.try5-opt.pdb edges SCWRLConform NameConform T0164.try5-opt-scwrl PrintConformPDB T0164.try5-opt-scwrl.pdb CostConform Time quit