SetSeed InfilePrefix // Note: the training atoms are needed for patching up chain breaks // when reading in conformations. InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/ ReadTrainingAtoms dunbrack-2191.atoms ReadRotamerLibrary dunbrack-2191.rot InFilePrefix /projects/compbio/experiments/undertaker/spots/ ReadAtomType exp-pdb.types ReadClashTable exp-pdb-2191-2symm.clash SetClashDefinition exp-pdb-2191-2symm CreateBurialCost near_backbone near-backbone-center.spot smoothed-near-backbone-2spot.hist near-backbone-count.spot CreateBurialCost way_back way-back-center.spot smoothed-way-back-2spot.hist way-back-count.spot CreateBurialCost dry5 monomeric-50pc-dry-5.spot smoothed-monomeric-50pc-dry-5.hist CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-6.5.hist CreateBurialCost dry8 monomeric-50pc-dry-8.spot smoothed-monomeric-50pc-dry-8.hist CreateBurialCost dry10 monomeric-50pc-dry-10.spot smoothed-monomeric-50pc-dry-10.hist CreateBurialCost dry12 monomeric-50pc-dry-12.spot smoothed-monomeric-50pc-dry-12.hist CreateAlphaCost alpha dunbrack-2191-alpha.hist CreateAlphaCost alpha_prev dunbrack-2191-alpha-1.hist -1 Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix # ReadTargetPDB T0353.blank.pdb ReadTargetSeq T0353.a2m 1 NameTarget T0353 PopConform InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix include try9.costfcn Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms // Edit this to include full sets of alignments from any // strongly-predicted superfamily // InfilePrefix 1xxxX/ // include read-alignments-scwrl.under ReadFragmentAlignment 1y8qA/T0353-1y8qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.3546e+00 ReadFragmentAlignment 1a26/T0353-1a26-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.0800e+00 ReadFragmentAlignment 1ffkI/T0353-1ffkI-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.9600e+00 ReadFragmentAlignment 1sgvA/T0353-1sgvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 7.1669e+00 ReadFragmentAlignment 2cybA/T0353-2cybA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 8.2540e+00 ReadFragmentAlignment 1t0hB/T0353-1t0hB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 8.2665e+00 ReadFragmentAlignment 1mdvA/T0353-1mdvA-t04-global-adpstyle1.a2m NOFILTER SCWRL force_alignment e_value 8.4140e+00 ReadFragmentAlignment 1a99A/T0353-1a99A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 8.7412e+00 ReadFragmentAlignment 1wr5A/T0353-1wr5A-t04-global-adpstyle1.a2m NOFILTER SCWRL force_alignment e_value 8.9921e+00 TryAllAlign shrink 0 min_keep_length 1 NameConform T0353.try9-al1 ReadFragmentAlignment 1y8qA/T0353-1y8qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 6.4776e-01 ReadFragmentAlignment 1a26/T0353-1a26-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.5500e+00 ReadFragmentAlignment 2cybA/T0353-2cybA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 6.4912e+00 ReadFragmentAlignment 2faoA/T0353-2faoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 7.3958e+00 ReadFragmentAlignment 1ffkI/T0353-1ffkI-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 7.7000e+00 ReadFragmentAlignment 1r3eA/T0353-1r3eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 8.2721e+00 ReadFragmentAlignment 1t0hB/T0353-1t0hB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 8.6101e+00 ReadFragmentAlignment 1a99A/T0353-1a99A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 8.8583e+00 ReadFragmentAlignment 1wr5A/T0353-1wr5A-t06-global-adpstyle1.a2m NOFILTER SCWRL force_alignment e_value 9.4965e+00 TryAllAlign shrink 0 min_keep_length 1 NameConform T0353.try9-al1A ReadFragmentAlignment 1y8qA/T0353-1y8qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.4553e+00 ReadFragmentAlignment 2faoA/T0353-2faoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 8.7066e+00 ReadFragmentAlignment 1t0hB/T0353-1t0hB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 8.9104e+00 ReadFragmentAlignment 2drpA/T0353-2drpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.0223e+01 ReadFragmentAlignment 1ffkI/T0353-1ffkI-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.0530e+01 ReadFragmentAlignment 1t3lA/T0353-1t3lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.1214e+01 ReadFragmentAlignment 2cybA/T0353-2cybA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.1335e+01 ReadFragmentAlignment 1mdvA/T0353-1mdvA-t2k-global-adpstyle1.a2m NOFILTER SCWRL force_alignment e_value 1.2007e+01 ReadFragmentAlignment 1y9kA/T0353-1y9kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.2602e+01 include 1a26/read-alignments-noscwrl.under include 1a99A/read-alignments-noscwrl.under include 1es6A/read-alignments-noscwrl.under include 1ffkI/read-alignments-noscwrl.under include 1iqtA/read-alignments-noscwrl.under include 1j0oA/read-alignments-noscwrl.under include 1jq4A/read-alignments-noscwrl.under include 1jzuA/read-alignments-noscwrl.under include 1mdvA/read-alignments-noscwrl.under include 1mg2D/read-alignments-noscwrl.under include 1nrfA/read-alignments-noscwrl.under include 1r3eA/read-alignments-noscwrl.under include 1sgvA/read-alignments-noscwrl.under include 1t0hB/read-alignments-noscwrl.under include 1t3lA/read-alignments-noscwrl.under include 1u7iA/read-alignments-noscwrl.under include 1wr5A/read-alignments-noscwrl.under include 1wtbA/read-alignments-noscwrl.under include 1xgsA/read-alignments-noscwrl.under include 1y8qA/read-alignments-noscwrl.under include 1y9kA/read-alignments-noscwrl.under include 1yemA/read-alignments-noscwrl.under include 2cdv/read-alignments-noscwrl.under include 2cthA/read-alignments-noscwrl.under include 2cybA/read-alignments-noscwrl.under include 2drpA/read-alignments-noscwrl.under include 2faoA/read-alignments-noscwrl.under include 2gtqA/read-alignments-noscwrl.under include 2mtaC/read-alignments-noscwrl.under TryAllAlign shrink 0 min_keep_length 1 NameConform T0353.try9-al2 ReadFragmentAlignment NOFILTER SCWRL all-align-edit.a2m InfilePrefix Time # ReportCost try9.rdb TryAllAlign shrink 0. min_keep_length 1 NameConform T0353.try9-al3 TryAllAlign shrink 0.2 min_keep_length 1 NameConform T0353.try9-al4 TryAllAlign shrink 0.3 min_keep_length 1 cumulative NameConform T0353.try9-al5 TryAllAlign shrink 0.4 min_keep_length 1 NameConform T0353.try9-al6 TryAllAlign shrink 0.5 min_keep_length 1 cumulative NameConform T0353.try9-al7 TryAllAlign shrink 0. min_keep_length 1 NameConform T0353.try9-al8 SCWRLConform NameConform T0353.try9 // Switch to the following (commenting out the TryAllAlign) // to polish existing models ## InfilePrefix decoys/ ## include read-pdb.under 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 T0353.t2k.many.frag ReadFragmentAlignment T0353.t04.many.frag ReadFragmentAlignment T0353.t06.many.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 \ FixOmega 0.3 \ HealPeptide 0.3 \ JiggleSubtree 0.3 \ JiggleSegment 0.3 \ OptSubtree 1 \ OptSegment 1 \ OptAllSegments 0.3 \ ShiftSubtree 0.3 \ ShiftSegment 0.3 \ TweakPhiSubtree 0.3 \ TweakPhiSegment 0.3 \ TweakPsiSubtree 0.3 \ TweakPsiSegment 0.3 \ TweakPsiPhiSubtree 0.3 \ TweakPsiPhiSegment 0.3 \ TweakHbondSubtree 0.3 \ TweakHbondSegment 0.3 \ TweakMultimer 0.3 \ TweakPeptide 0.3 \ OneRotamer 1 \ ClashingRotamer 1 \ ClusteredRotamer 2 \ ReduceBreak 5 \ CloseGap 5 \ HealGap 5 \ MoveGap 5 \ ReduceConstraint 5 \ ImproveSSBond 0 \ InsertSSBond 0 \ InsertAlignment 1 \ InsertSpecificFragment 20 \ InsertFragment 5 \ TwoFragment 5 \ CrossOver 3 \ CrossAndInsert 5 \ ReduceClash 5 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 5 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0353.try9-opt1 PrintConformPDB T0353.try9-opt1.pdb SCWRLConform NameConform T0353.try9-opt1-scwrl PrintConformPDB T0353.try9-opt1-scwrl.pdb CostConform Time InitMethodProbs \ FixOmega 1 \ OneRotamer 5 \ ClashingRotamer 1 \ ClusteredRotamer 1 \ CrossOver 1 \ CrossAndInsert 1\ CloseGap 1 \ MoveGap 1 \ HealGap 2 \ InsertFragment 1 \ InsertSpecificFragment 2 \ ReduceBreak 2 \ ReduceConstraint 2 \ ReduceClash 1 \ JiggleSegment 1 \ JiggleSubtree 1 \ OptAllSegments 1 \ OptSegment 1 \ OptSubtree 1 \ ShiftSegment 1 \ ShiftSubtree 1 \ TweakHbondSegment 1 \ TweakHbondSubtree 1 \ TweakPhiSegment 1 \ TweakPhiSubtree 1 \ TweakPsiSegment 1 \ TweakPsiSubtree 1 \ TweakPsiPhiSegment 1 \ TweakPsiPhiSubtree 1 CostConform OptConform pool_size 40 num_gen 60 gen_size 100 \ super_iter 2 super_num_gen 300 use_all NameConform T0353.try9-opt2 PrintConformPDB T0353.try9-opt2.pdb # PrintConformHbonds try9-opt2.all-hbonds # PrintConformHbonds nonhelix backbone try9-opt2.beta-hbonds PrintConformSheets try9-opt2.sheets PrintConformHelices try9-opt2.helices PrintConstraints all try9-opt2.constraints # PrintConformBreaks try9-opt2.breaks CostConform Time quit