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 T0308.blank.pdb ReadTargetSeq T0308.a2m 1 NameTarget T0308 PopConform InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix include try1.costfcn Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms Include T0308.t04.undertaker-align.under Include T0308.t06.undertaker-align.under Include T0308.t2k.undertaker-align.under Include T0308.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 Time // Switch to the following (commenting out the TryAllAlign) // to polish existing models InfilePrefix decoys/ # include read-pdb.under ReadConformPDB T0308.try6-opt1-scwrl.pdb ReadConformPDB T0308.try6-opt1.pdb ReadConformPDB T0308.try6-opt2.gromacs0.pdb ReadConformPDB T0308.try6-opt2.gromacs0.repack-nonPC.pdb ReadConformPDB T0308.try6-opt2.pdb ReadConformPDB T0308.try6-opt2.repack-nonPC.pdb ReadConformPDB tr308-scwrl.pdb ReadConformPDB tr308.pdb 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 T0308.t2k.many.frag ReadFragmentAlignment T0308.t04.many.frag ReadFragmentAlignment T0308.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 1 \ OneRotamer 5 \ HealPeptide 1 \ ClashingRotamer 5 \ ClusteredRotamer 1 \ CrossOver 1 \ CrossAndInsert 1\ CloseGap 1 \ MoveGap 1 \ HealGap 1 \ InsertFragment 1 \ InsertSpecificFragment 2 \ ImproveSSBond 0 \ InsertSSBond 0 \ InsertAlignment 1 \ ReduceBreak 1 \ ReduceConstraint 1 \ 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 \ TweakPeptide 2 OptConform pool_size 20 num_gen 100 gen_size 100 \ super_iter 5 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0308.try7-opt1 PrintConformPDB T0308.try7-opt1.pdb SCWRLConform NameConform T0308.try7-opt1-scwrl PrintConformPDB T0308.try7-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 200 \ super_iter 2 super_num_gen 300 use_all NameConform T0308.try7-opt2 PrintConformPDB T0308.try7-opt2.pdb # PrintConformHbonds try7-opt2.all-hbonds # PrintConformHbonds nonhelix backbone try7-opt2.beta-hbonds PrintConformSheets try7-opt2.sheets PrintConformHelices try7-opt2.helices PrintConstraints all try7-opt2.constraints # PrintConformBreaks try7-opt2.breaks CostConform Time quit