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 T0296.blank.pdb ReadTargetSeq T0296.a2m 1 NameTarget T0296 PopConform InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix include try8.costfcn Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms # I am dubious of t04 and t06 alignments here # Include T0296.t04.undertaker-align.under # Include T0296.t06.undertaker-align.under # Include T0296.t2k.undertaker-align.under # Include T0296.undertaker-align.under # ReadFragmentAlignment NOFILTER SCWRL all-align.a2m // Edit this to include full sets of alignments from any // strongly-predicted superfamily // InfilePrefix 1xxxX/ // include read-alignments-scwrl.under InfilePrefix 1j0dA/ include read-alignments-scwrl.under InfilePrefix 1bksB/ include read-alignments-scwrl.under InfilePrefix 1p5jA/ include read-alignments-scwrl.under InfilePrefix 1qopB/ include read-alignments-scwrl.under InfilePrefix 1kl7A/ include read-alignments-scwrl.under InfilePrefix TryAllAlign shrink 0 min_keep_length 1 NameConform T0296.try8-al1 Time # ReportCost try8.rdb NameConform T0296.try8-al1A InfilePrefix 1a50B/ include read-alignments-scwrl.under InfilePrefix 2tysB/ include read-alignments-scwrl.under InfilePrefix 1k8yB/ include read-alignments-scwrl.under InfilePrefix 2wsyB/ include read-alignments-scwrl.under InfilePrefix 1e5xA/ include read-alignments-scwrl.under InfilePrefix TryAllAlign shrink 0 min_keep_length 1 NameConform T0296.try8-al2 # for try4, I'm commenting these out. They may just confuse things # in for Try5, back out for Try6... # and back in again for Try7 # and out... # ReadConformPDB decoys/servers/forecast-s_AL1.pdb.gz # ReadConformPDB decoys/servers/FORTE2_AL1.pdb.gz # ReadConformPDB decoys/servers/karypis.srv.2_TS3.pdb.gz # ReadConformPDB decoys/servers/kABIpro_TS1 # ReadConformPDB decoys/servers/FUNCTION_TS3 # InfilePrefix # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0296.try8-al2A TryAllAlign shrink 0. min_keep_length 1 NameConform T0296.try8-al3 TryAllAlign shrink 0.2 min_keep_length 1 NameConform T0296.try8-al4 TryAllAlign shrink 0.3 min_keep_length 1 cumulative NameConform T0296.try8-al5 TryAllAlign shrink 0.4 min_keep_length 1 NameConform T0296.try8-al6 TryAllAlign shrink 0.5 min_keep_length 1 cumulative NameConform T0296.try8-al7 TryAllAlign shrink 0. min_keep_length 1 NameConform T0296.try8-al8 SCWRLConform NameConform T0296.try8 // 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 T0296.t2k.many.frag ReadFragmentAlignment T0296.t04.many.frag ReadFragmentAlignment T0296.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 \ 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 T0296.try8-opt1 PrintConformPDB T0296.try8-opt1.pdb SCWRLConform NameConform T0296.try8-opt1-scwrl PrintConformPDB T0296.try8-opt1-scwrl.pdb CostConform Time InitMethodProbs \ 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 T0296.try8-opt2 PrintConformPDB T0296.try8-opt2.pdb # PrintConformHbonds try8-opt2.all-hbonds # PrintConformHbonds nonhelix backbone try8-opt2.beta-hbonds PrintConformSheets try8-opt2.sheets PrintConformHelices try8-opt2.helices PrintConstraints all try8-opt2.constraints # PrintConformBreaks try8-opt2.breaks CostConform Time quit