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 T0204.blank.pdb NameTarget T0204 PopConform InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix CreatePredAlphaCost pred_alpha2 alpha11 T0204.t2k.alpha.rdb 2 alpha alpha_prev sum include try13.costfcn Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms # Include T0204.t2k.undertaker-align.under // get specific ones below. also, contents of this file are obsolete # // because of missing t04 and t2k in filenames # ReadFragmentAlignment NOFILTER T0204.t2k-2track-undertaker.a2m // Edit this to include full sets of alignments from any // strongly-predicted superfamily InfilePrefix 1emsA/ include read-alignments.under InfilePrefix 1fit/ include read-alignments.under InfilePrefix 1gupA/ include read-alignments.under InfilePrefix 1guqA/ include read-alignments.under InfilePrefix 1hxpA/ include read-alignments.under InfilePrefix 1hxqA/ include read-alignments.under InfilePrefix 1hxqB/ include read-alignments.under InfilePrefix 1kpeA/ include read-alignments.under InfilePrefix 1kpf/ include read-alignments.under InfilePrefix 1rzyA/ include read-alignments.under InfilePrefix 2fhi/ include read-alignments.under InfilePrefix 4rhn/ include read-alignments.under InfilePrefix Time # ReportCost try13.rdb # TryAllAlign shrink 0.4 min_keep_length 1 # NameConform T0204.try13-al1 # TryAllAlign shrink 0.4 min_keep_length 1 cumulative # NameConform T0204.try13-al2 # # TryAllAlign shrink 0. min_keep_length 1 # NameConform T0204.try13-al3 # TryAllAlign shrink 0. min_keep_length 1 cumulative # NameConform T0204.try13-al4 # # # TryAllAlign shrink 0.3 min_keep_length 4 # NameConform T0204.try13-al5 # TryAllAlign shrink 0.3 min_keep_length 4 cumulative # NameConform T0204.try13-al6 # # TryAllAlign shrink 0.1 min_keep_length 2 # NameConform T0204.try13-al7 # TryAllAlign shrink 0.1 min_keep_length 2 cumulative # NameConform T0204.try13-al8 # start from all 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 T0204.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 4 \ ClashingRotamer 4 \ ClusteredRotamer 5 \ InsertFragment 5 \ CrossOver 10 \ CrossAndInsert 5 \ TwoFragment 5 \ InsertSpecificFragment 4 \ ReduceBreak 4 \ HealGap 4 \ CloseGap 4 \ ReduceConstraint 1 \ ReduceClash 5 \ JiggleSegment 1 \ JiggleSubtree 1 \ OptAllSegments 1 \ OptSegment 1 \ OptSubtree 1 \ TweakHbondSegment 1 \ TweakHbondSubtree 1 \ TweakPhiSegment 1 \ TweakPhiSubtree 1 \ TweakPsiSegment 1 \ TweakPsiSubtree 1 \ TweakPsiPhiSegment 1 \ TweakPsiPhiSubtree 1 \ InsertSSBond 0 \ ImproveSSBond 0 SCWRLConform NameConform T0204.try13 OptConform pool_size 60 num_gen 50 gen_size 180 \ super_iter 4 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0204.try13-opt1 PrintConformPDB T0204.try13-opt1.pdb Time SCWRLConform NameConform T0204.try13-opt1-scwrl PrintConformPDB T0204.try13-opt1-scwrl.pdb CostConform Time InitMethodProbs \ OneRotamer 8 \ ClashingRotamer 3 \ ClusteredRotamer 3 \ CrossOver 10 \ CrossAndInsert 1\ CloseGap 1 \ MoveGap 1 \ HealGap 2 \ InsertFragment 1 \ InsertSpecificFragment 2 \ ReduceBreak 2 \ ReduceConstraint 1 \ ReduceClash 1 \ JiggleSegment 1 \ JiggleSubtree 1 \ OptSegment 1 \ OptAllSegments 1 \ OptSubtree 1 \ TweakHbondSegment 1 \ TweakHbondSubtree 1 \ TweakPhiSegment 1 \ TweakPhiSubtree 1 \ TweakPsiPhiSegment 1 \ TweakPsiPhiSubtree 1 \ TweakPsiSegment 1 \ TweakPsiSubtree 1 CostConform OptConform pool_size 100 num_gen 50 gen_size 150 \ super_iter 2 super_num_gen 400 use_all NameConform T0204.try13-opt2 PrintConformPDB T0204.try13-opt2.pdb PrintConformSheets try13.sheets PrintConstraints all try13-opt2.constraints PrintConformBreaks try13-opt2.breaks CostConform Time quit