// To be run from pce/casp5/t0185 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ // ConformFromSeq replace // get a random conformation, removing all-zero one // NameConform T0185.rand // Time InFilePrefix ReadTemplateAtoms Template.atoms Include T0185.t2k.undertaker-align.script ReadFragmentAlignment T0185.t2k-2track-undertaker.a2m InfilePrefix 1uag/ include read-alignments.under InfilePrefix 3uagA/ include read-alignments.under InfilePrefix 4uagA/ include read-alignments.under InfilePrefix 1e8cA/ include read-alignments.under InfilePrefix 1gg4A/ include read-alignments.under InfilePrefix 1jbwA/ include read-alignments.under InfilePrefix Time // Note: the try3 run was accidentally run with try2 naming // ReadConformPdb decoys/T0185.try2-al4.pdb // NameConform T0185.try4-try3-al3 // ReadConformPdb decoys/T0185.try4-opt.pdb // NameConform T0185.try5-try4 ReadConformPdb decoys/T0185.try4-opt.pdb NameConform T0185.try6-try4 ReadConformPdb decoys/T0185.try5-opt.pdb NameConform T0185.try6-try5 ReportCost undertaker-try6.rdb // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0185.try6-al2 // PrintConformPDB T0185.try6-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0185.try6-al4 // PrintConformPDB T0185.try6-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0185.try6-al6 // PrintConformPDB T0185.try6-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0185.try6-al8 // PrintConformPDB T0185.try6-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0185.try6-al10 // PrintConformPDB T0185.try6-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0185.try6-al12 // PrintConformPDB T0185.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 T0185.t2k.frag ReadFragmentAlignment t0185-1-100/T0185.t2k.frag ReadFragmentAlignment t0185-81-300/T0185.t2k.frag ReadFragmentAlignment t0185-301-457/T0185.t2k.frag ReadFragmentAlignment t0185-351-400/T0185.t2k.frag InfilePrefix 1fgs/ include read-alignments.under InfilePrefix 1eehA/ include read-alignments.under InfilePrefix t0185-1-100/1uag/ include read-alignments.under InfilePrefix t0185-1-100/3uagA/ include read-alignments.under InfilePrefix t0185-1-100/4uagA/ include read-alignments.under InfilePrefix t0185-1-100/1eehA/ include read-alignments.under InfilePrefix t0185-1-100/1bg6/ include read-alignments.under InfilePrefix t0185-1-100/1i36A/ include read-alignments.under InfilePrefix t0185-1-100/1f8gA/ include read-alignments.under InfilePrefix t0185-1-100/1guzA/ include read-alignments.under InfilePrefix t0185-1-100/1gosA/ include read-alignments.under InfilePrefix t0185-1-100/1pjbA/ include read-alignments.under InfilePrefix t0185-1-100/1nhp/ include read-alignments.under InfilePrefix t0185-1-100/1ceqA/ include read-alignments.under InfilePrefix t0185-1-100/1lldA/ include read-alignments.under InfilePrefix t0185-81-300/1uag/ include read-alignments.under InfilePrefix t0185-81-300/4uagA/ include read-alignments.under InfilePrefix t0185-81-300/3uagA/ include read-alignments.under InfilePrefix t0185-81-300/1e8cA/ include read-alignments.under InfilePrefix t0185-81-300/1gg4A/ include read-alignments.under InfilePrefix t0185-81-300/1jbwA/ include read-alignments.under InfilePrefix t0185-81-300/1fgs/ include read-alignments.under InfilePrefix t0185-301-457/1e8cA/ include read-alignments.under InfilePrefix t0185-301-457/1jbwA/ include read-alignments.under InfilePrefix t0185-301-457/1fgs/ include read-alignments.under InfilePrefix t0185-301-457/1uag/ include read-alignments.under InfilePrefix t0185-301-457/3uagA/ include read-alignments.under InfilePrefix t0185-301-457/4uagA/ include read-alignments.under InfilePrefix t0185-301-457/1gg4A/ include read-alignments.under InfilePrefix t0185-301-457/1g0oA/ include read-alignments.under InfilePrefix t0185-301-457/1ybvA/ include read-alignments.under InfilePrefix t0185-301-457/1qisA/ include read-alignments.under InfilePrefix t0185-351-400/1qeyA/ include read-alignments.under InfilePrefix t0185-351-400/1caj/ include read-alignments.under InfilePrefix t0185-351-400/2cba/ include read-alignments.under InfilePrefix t0185-351-400/1ydd/ include read-alignments.under InfilePrefix t0185-351-400/1yda/ include read-alignments.under InfilePrefix t0185-351-400/1hea/ include read-alignments.under InfilePrefix t0185-351-400/1heb/ include read-alignments.under InfilePrefix t0185-351-400/1fr7A/ include read-alignments.under InfilePrefix t0185-351-400/1fr7A/ include read-alignments.under InFilePrefix // 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 0.5 \ OneRotamer 0.01 \ InsertFragment 8 \ CrossOver 0 \ CrossAndInsert 3 \ TwoFragment 20 \ InsertSpecificFragment 7 \ ReduceBreak 5 \ CloseGap 0.3 \ ReduceClash 1 \ ReduceConstraint 1 \ JiggleSubtree 0.01 \ OptSubtree 0.03 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0185.try6 OptConform pool_size 40 num_gen 150 gen_size 180 super_iter 1 \ pdb use_all // scwrl_each NameConform T0185.try6-opt PrintConformPDB T0185.try6-opt.pdb edges // SCWRLConform // NameConform T0185.try6-opt-scwrl // PrintConformPDB T0185.try6-opt-scwrl.pdb CostConform Time quit