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-1332.atoms ReadRotamerLibrary dunbrack-1332.rot InFilePrefix /projects/compbio/experiments/undertaker/spots/ # ReadAtomType pdb-name.types # ReadClashTable pdb-1332-2symm.clash # SetClashDefinition pdb-2symm ReadAtomType exp-pdb.types ReadClashTable exp-pdb-1332-2symm.clash SetClashDefinition exp-pdb-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-1332-alpha.hist CreateAlphaCost alpha_prev dunbrack-1332-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 T0197.blank.pdb NameTarget T0197 PopConform InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix include tryB23.costfcn Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms // Include T0197.t2k.undertaker-align.under // ReadFragmentAlignment NOFILTER T0197.t2k-2track-undertaker.a2m // SCWRL keyword omitted from all-align, because SCWRL // was taking too long on some alignments. ReadFragmentAlignment NOFILTER all-align.a2m // Edit this to include full sets of alignments from any // strongly-predicted superfamily ## InfilePrefix 1gm6A/ ## include read-alignments.under ## InfilePrefix 1d8hA/ ## include read-alignments.under ## InfilePrefix 1d8iA/ ## include read-alignments.under ## InfilePrefix 1cjxA/ ## include read-alignments.under ## InfilePrefix 1fa8A/ ## include read-alignments.under ## InfilePrefix 1f9zA/ ## include read-alignments.under ## InfilePrefix 1dzkA/ ## include read-alignments.under ## InfilePrefix 1bj7/ ## include read-alignments.under ## InfilePrefix 1aisA/ ## include read-alignments.under InfilePrefix Time # ReportCost tryB23.rdb ## TryAllAlign shrink 0.4 min_keep_length 1 ## NameConform T0197.tryB23-al1 ## TryAllAlign shrink 0.4 min_keep_length 1 cumulative ## NameConform T0197.tryB23-al2 ## TryAllAlign shrink 0. min_keep_length 1 ## NameConform T0197.tryB23-al3 ## TryAllAlign shrink 0. min_keep_length 1 cumulative ## NameConform T0197.tryB23-al4 ## TryAllAlign shrink 0.3 min_keep_length 4 ## NameConform T0197.tryB23-al5 ## TryAllAlign shrink 0.3 min_keep_length 4 cumulative ## NameConform T0197.tryB23-al6 ## TryAllAlign shrink 0.1 min_keep_length 2 ## NameConform T0197.tryB23-al7 ## TryAllAlign shrink 0.1 min_keep_length 2 cumulative ## NameConform T0197.tryB23-al8 # This is an attempt to polish tryB19, so don't include # any models that currently score better than it. InfilePrefix decoys/ ReadConformPDB T0197.try7-opt2.pdb NameConform try7-tryB23 ReadConformPDB T0197.try8-opt2.pdb NameConform try8-tryB23 ReadConformPDB T0197.try9-opt2.pdb NameConform try9-tryB23 ReadConformPDB T0197.try10-opt2.pdb NameConform try10-tryB23 ReadConformPDB T0197.try11-opt2.pdb NameConform try11-tryB23 ReadConformPDB T0197.try11-opt2.pdb NameConform try12-tryB23 ReadConformPDB T0197.tryB14-opt2.pdb NameConform tryB14-tryB23 ReadConformPDB T0197.tryB15-opt2.pdb NameConform tryB15-tryB23 ReadConformPDB T0197.tryB16-opt2.pdb NameConform tryB16-tryB23 ReadConformPDB T0197.tryB18-opt2.pdb NameConform tryB18-tryB23 ReadConformPDB T0197.tryB19-opt2.pdb NameConform tryB19-tryB23 ReadConformPDB T0197.tryB20-opt2.pdb NameConform tryB20-tryB23 ReadConformPDB T0197.tryB21-opt2.pdb NameConform tryB21-tryB23 ReadConformPDB T0197.tryB22-opt2.pdb NameConform tryB21-tryB23 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 T0197.t2k.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 InsertAlignment 1 \ OneRotamer 1 \ ClashingRotamer 1 \ ClusteredRotamer 2 \ InsertFragment 10 \ CrossOver 25 \ CrossAndInsert 5 \ TwoFragment 5 \ InsertSpecificFragment 15 \ ReduceBreak 5 \ HealGap 5 \ CloseGap 5 \ ReduceConstraint 20 \ ReduceClash 5 \ JiggleSegment 0.3 \ JiggleSubtree 0.3 \ OptSegment 3 \ OptSubtree 3 \ OptAllSegments 3 \ TweakHbondSegment 0.3 \ TweakHbondSubtree 0.3 \ TweakPhiSegment 0.3 \ TweakPhiSubtree 0.3 \ TweakPsiSegment 0.3 \ TweakPsiSubtree 0.3 \ InsertSSBond 0 \ ImproveSSBond 0 SCWRLConform NameConform T0197.tryB23 OptConform pool_size 20 num_gen 50 gen_size 150 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0197.tryB23-opt1 PrintConformPDB T0197.tryB23-opt1.pdb SCWRLConform NameConform T0197.tryB23-opt1-scwrl PrintConformPDB T0197.tryB23-opt1-scwrl.pdb CostConform Time InitMethodProbs \ OneRotamer 5 \ ClashingRotamer 1 \ ClusteredRotamer 1 \ CrossOver 5 \ CrossAndInsert 1\ CloseGap 1 \ MoveGap 1 \ HealGap 2 \ InsertFragment 1 \ InsertSpecificFragment 2 \ ReduceBreak 2 \ ReduceConstraint 5 \ ReduceClash 1 \ JiggleSegment 1 \ JiggleSubtree 1 \ OptAllSegments 1 \ OptSegment 1 \ OptSubtree 1 \ OptAllSegments 1 \ TweakHbondSegment 1 \ TweakHbondSubtree 1 \ TweakPhiSegment 1 \ TweakPhiSubtree 1 \ TweakPsiSegment 1 \ TweakPsiSubtree 1 CostConform OptConform pool_size 200 num_gen 50 gen_size 250 \ super_iter 1 super_num_gen 40 use_all NameConform T0197.tryB23-opt2 PrintConformPDB T0197.tryB23-opt2.pdb PrintConformSheets tryB23-opt2.sheets PrintConstraints all tryB23-opt2.constraints PrintConformBreaks tryB23-opt2.breaks CostConform quit