// To be run from pce/casp5/t0172 SetSeed InfilePrefix Include define-score.script Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ ConformFromSeq replace // get a random conformation, removing all-zero one NameConform T0172.rand Time InFilePrefix ReadTemplateAtoms Template.atoms ReadFragmentAlignment T0172-superfamily.a2m ReadFragmentAlignment T0172-1dusA.vast.a2m // include full-align.under include mid-align.under Time // ReadConformPDB decoys/T0172.cut-and-paste.pdb // NameConform T0172.try5-cut // ReadConformPDB decoys/T0172.try1-al2.pdb // NameConform T0172.try6-try1-al2 // ReadConformPDB decoys/T0172.try2.0.30.pdb // NameConform T0172.try6-try2-0 // ReadConformPDB decoys/T0172.try3.22.25.pdb // NameConform T0172.try6-try3-22 // ReadConformPDB decoys/T0172.try4-opt-scwrl.pdb // NameConform T0172.try6-try4 // ReadConformPDB decoys/T0172.try5-opt-scwrl.pdb // NameConform T0172.try6-try5 // ReadConformPDB decoys/T0172-moved6.pdb // NameConform T0172.try7-moved // ReadConformPDB decoys/T0172.try3.22.25.pdb // NameConform T0172.try8-try3-22 // ReadConformPDB decoys/T0172.try4-opt-scwrl.pdb // NameConform T0172.try8-try4 // ReadConformPDB decoys/T0172.try5-opt-scwrl.pdb // NameConform T0172.try8-try5 // ReadConformPDB decoys/T0172.try6-opt-scwrl.pdb // NameConform T0172.try8-try6 // ReadConformPDB decoys/T0172.try7-opt.pdb // NameConform T0172.try8-try7 // ReadConformPDB decoys/T0172-moved8.pdb // NameConform T0172.try9-moved // ReadConformPDB decoys/T0172.try9-opt.pdb // NameConform T0172.try10-try9 // ReadConformPDB decoys/T0172.try6-opt-scwrl.pdb // NameConform T0172.try11-try6 // ReadConformPDB decoys/T0172.try7-opt-scwrl.pdb // NameConform T0172.try11-try7 // ReadConformPDB decoys/T0172.try8-opt.pdb // NameConform T0172.try11-try8 // ReadConformPDB decoys/T0172.try9-opt.pdb // NameConform T0172.try11-try9 // ReadConformPDB decoys/T0172.try10-opt.pdb // NameConform T0172.try11-try10 // ReadConformPDB decoys/T0172.try4.7.25.pdb // NameConform T0172.try12-try4-7 // ReadConformPDB decoys/T0172.try6.4.100.pdb // NameConform T0172.try12-try6-4 // ReadConformPDB decoys/T0172.try7-opt-scwrl.pdb // NameConform T0172.try12-try7 // ReadConformPDB decoys/T0172.try8-try6.2.80.pdb // NameConform T0172.try12-try8-2 // ReadConformPDB decoys/T0172.try9.3.20.pdb // NameConform T0172.try12-try9-3 // ReadConformPDB decoys/T0172.try10-opt.pdb // NameConform T0172.try12-try10 // ReadConformPDB decoys/T0172.try11-opt.pdb // NameConform T0172.try13-try11 // ReadConformPDB decoys/T0172.try11-try8.0.100.pdb // NameConform T0172.try13-try11-0 // ReadConformPDB decoys/T0172.try10-opt.pdb // NameConform T0172.try13-try10 // ReadConformPDB decoys/T0172.try10.0.40.pdb // NameConform T0172.try13-try10-0 // ReadConformPDB decoys/T0172.try9.4.20.pdb // NameConform T0172.try13-try9-4 // ReadConformPDB decoys/T0172.try9-opt-scwrl.pdb // NameConform T0172.try13-try9-s // ReadConformPDB decoys/T0172.try9-opt.pdb // NameConform T0172.try13-try9 // ReadConformPDB decoys/T0172.try8-try6.0.80.pdb // NameConform T0172.try13-try8-0 // ReadConformPDB decoys/T0172.try8-try6.3.80.pdb // NameConform T0172.try13-try8-3 // ReadConformPDB decoys/T0172.try8-opt.pdb // NameConform T0172.try13-try8 // ReadConformPDB decoys/T0172.try7-opt-scwrl.pdb // NameConform T0172.try13-try7 // ReadConformPDB decoys/T0172.try6-opt-scwrl.pdb // NameConform T0172.try13-try6 // ReadConformPDB decoys/T0172.try5-opt-scwrl.pdb // NameConform T0172.try13-try5 // ReadConformPDB decoys/T0172.try4.9.25.pdb // NameConform T0172.try13-try4-9 // ReadConformPDB decoys/T0172.try11-opt.pdb // NameConform T0172.try14-try11 // ReadConformPDB decoys/T0172.try11-try8.0.100.pdb // NameConform T0172.try14-try11-0 // ReadConformPDB decoys/T0172.try10-opt.pdb // NameConform T0172.try14-try10 // ReadConformPDB decoys/T0172.try10.0.40.pdb // NameConform T0172.try14-try10-0 // ReadConformPDB decoys/T0172.try9.4.20.pdb // NameConform T0172.try14-try9-4 // ReadConformPDB decoys/T0172.try9-opt-scwrl.pdb // NameConform T0172.try14-try9-s // ReadConformPDB decoys/T0172.try9-opt.pdb // NameConform T0172.try14-try9 // ReadConformPDB decoys/T0172.try8-try6.0.80.pdb // NameConform T0172.try14-try8-0 // ReadConformPDB decoys/T0172.try8-try6.3.80.pdb // NameConform T0172.try14-try8-3 // ReadConformPDB decoys/T0172.try8-opt.pdb // NameConform T0172.try14-try8 // ReadConformPDB decoys/T0172.try7-opt-scwrl.pdb // NameConform T0172.try14-try7 // ReadConformPDB decoys/T0172.try6-opt-scwrl.pdb // NameConform T0172.try14-try6 // ReadConformPDB decoys/T0172.try5-opt-scwrl.pdb // NameConform T0172.try14-try5 // ReadConformPDB decoys/T0172.try4.9.25.pdb // NameConform T0172.try14-try4-9 // ReadConformPDB decoys/T0172.try13-try9.0.120.pdb // NameConfrom T0172.try15-try13-0 // ReadConformPDB decoys/T0172.try14-try10-0.2.120.pdb // NameConfrom T0172.try15-try14-2 // ReadConformPDB decoys/T0172.try14-try10-0.3.120.pdb // NameConfrom T0172.try15-try14-3 // ReadConformPDB decoys/T0172.try14-opt.pdb // NameConfrom T0172.try15-try14 // ReadConformPDB decoys/T0172.cut-and-paste.pdb // NameConfrom T0172.try16-cut // ReadConformPDB decoys/T0172.try9-opt.pdb // NameConfrom T0172.try16-try9 // ReadConformPDB decoys/T0172.try14-opt.pdb // NameConfrom T0172.try16-try14 // ReadConformPDB decoys/T0172.try15-opt.pdb // NameConfrom T0172.try16-try15 // ReadConformPDB decoys/T0172.try15-opt.pdb // NameConform T0172.try20-try15 //ReadConformPDB decoys/T0172.try15-opt.pdb // NameConform T0172.try21-try15 //ReadConformPDB decoys/T0172.try20.0.50.pdb // NameConform T0172.try21-try20-0 //ReadConformPDB decoys/T0172.try15-opt.pdb.4.100.pdb // NameConform T0172.try21-try16-4 //ReadConformPDB decoys/T0172.try15-opt.pdb.3.100.pdb // NameConform T0172.try21-try16-3 // ReadConformPDB decoys/T0172.try15-opt-scwrl.pdb // NameConform T0172.try22-try15 // ReadConformPDB decoys/T0172.try20-opt.pdb // NameConform T0172.try22-try20 // ReadConformPDB decoys/T0172.try10-opt.pdb // NameConform T0172.try22-try10 // ReadConformPDB decoys/T0172.try21-opt.pdb // NameConform T0172.try22-try21 // ReadConformPDB decoys/T0172.try21-opt.pdb // NameConform T0172.try23-try21 // ReadConformPDB decoys/T0172.try22-opt.pdb // NameConform T0172.try23-try22 // ReadConformPDB decoys/T0172.try21-opt.pdb // NameConform T0172.try24-try21 // ReadConformPDB decoys/T0172.try22-opt.pdb // NameConform T0172.try24-try22 // ReadConformPDB decoys/T0172.try23-opt.pdb // NameConform T0172.try24-try23 // ReadConformPDB decoys/T0172.try22-opt.pdb // NameConform T0172.try25-try22 // ReadConformPDB decoys/T0172.try23-opt.pdb // NameConform T0172.try25-try23 // ReadConformPDB decoys/T0172.try24-opt.pdb // NameConform T0172.try25-try24 // ReadConformPDB decoys/T0172.try23-opt.pdb // NameConform T0172.try26-try23 // ReadConformPDB decoys/T0172.try24-opt.pdb // NameConform T0172.try26-try24 // ReadConformPDB decoys/T0172.try25-opt.pdb // NameConform T0172.try26-try25 // ReadConformPDB decoys/T0172.try23-opt.pdb // NameConform T0172.try27-try23 // ReadConformPDB decoys/T0172.try24-opt.pdb // NameConform T0172.try27-try24 // ReadConformPDB decoys/T0172.try25-opt.pdb // NameConform T0172.try27-try25 // ReadConformPDB decoys/T0172-moved27.pdb // NameConform T0172.try28-moved // ReadConformPDB decoys/T0172.try24-opt.pdb // NameConform T0172.try29-try24 // ReadConformPDB decoys/T0172.try25-opt.pdb // NameConform T0172.try29-try25 // ReadConformPDB decoys/T0172.try28-opt.pdb // NameConform T0172.try29-try28 // ReadConformPDB decoys/T0172.try27-opt.pdb // NameConform T0172.try29-try27 ReadConformPDB decoys/T0172.try28-opt.pdb NameConform T0172.try30-try28 ReportCost undertaker-try30.rdb // ConformFromSeq replace // get a random conformation, removing all-zero one // ConformFromSeq // don't replace good conformations // NameConform T0172.rand Time // TryAllAlign shrink 0.4 min_keep_length 5 // TryAllAlign shrink 0.4 min_keep_length 5 cumulative // NameConform T0172.try30-al2 // PrintConformPDB T0172.try30-al2.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0172.try30-al4 // PrintConformPDB T0172.try30-al4.pdb edges // TryAllAlign shrink 0.3 min_keep_length 4 // TryAllAlign shrink 0.3 min_keep_length 4 cumulative // NameConform T0172.try30-al6 // PrintConformPDB T0172.try30-al6.pdb edges // TryAllAlign shrink 0.1 min_keep_length 2 // TryAllAlign shrink 0.1 min_keep_length 2 cumulative // NameConform T0172.try30-al8 // PrintConformPDB T0172.try30-al8.pdb edges // TryAllAlign shrink 0.2 min_keep_length 3 // TryAllAlign shrink 0.2 min_keep_length 3 cumulative // NameConform T0172.try30-al10 // PrintConformPDB T0172.try30-al10.pdb edges // TryAllAlign shrink 0. min_keep_length 1 // TryAllAlign shrink 0. min_keep_length 1 cumulative // NameConform T0172.try30-al12 // PrintConformPDB T0172.try30-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 T0172.t2k.frag ReadFragmentAlignment t0172-106-222/T0172.t2k.frag // Include the full-align.under alignments either here or at the // beginning, not both. include full-align.under // 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 0.01 \ OneRotamer 0.04 \ InsertFragment 5 \ CrossOver 0 \ CrossAndInsert 1 \ TwoFragment 15 \ InsertSpecificFragment 10 \ ReduceBreak 0.1 \ CloseGap 0.2 \ ReduceConstraint 5 \ ReduceClash 0.3 \ JiggleSubtree 0.04 \ OptSubtree 0.2 \ InsertSSBond 0 \ ImproveSSBond 0 NameConform T0172.try30 OptConform pool_size 70 num_gen 100 gen_size 200 super_iter 1 \ use_all pdb // scwrl_each // no_initial_fill NameConform T0172.try30-opt PrintConformPDB T0172.try30-opt.pdb edges // SCWRLConform // NameConform T0172.try30-opt-scwrl // PrintConformPDB T0172.try30-opt-scwrl.pdb CostConform Time quit