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 T0272.blank.pdb NameTarget T0272 PopConform InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix include try21.costfcn Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms # Include T0272.t2k.undertaker-align.under # ReadFragmentAlignment NOFILTER T0272.t2k-2track-undertaker.a2m ReadFragmentAlignment NOFILTER all-align.a2m // Edit this to include full sets of alignments from any // strongly-predicted superfamily // InfilePrefix 1xxxX/ // include read-alignments.under InfilePrefix Time # ReportCost try21.rdb # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0272.try21-al1 # TryAllAlign shrink 0.6 min_keep_length 1 cumulative # NameConform T0272.try21-al2 # TryAllAlign shrink 0. min_keep_length 1 # NameConform T0272.try21-al3 # TryAllAlign shrink 0.2 min_keep_length 1 # NameConform T0272.try21-al4 # TryAllAlign shrink 0.3 min_keep_length 1 cumulative # NameConform T0272.try21-al5 # TryAllAlign shrink 0.4 min_keep_length 1 # NameConform T0272.try21-al6 # TryAllAlign shrink 0.5 min_keep_length 1 cumulative # NameConform T0272.try21-al7 # TryAllAlign shrink 0. min_keep_length 1 # NameConform T0272.try21-al8 # SCWRLConform # NameConform T0272.try21 // Switch to the following (commenting out the TryAllAlign) // to polish existing models InfilePrefix decoys/ # include read-pdb.under ReadConformPDB T0272.try1-opt2.repack-nonPC.pdb ReadConformPDB T0272.try10-opt2.repack-nonPC.pdb ReadConformPDB T0272.try11-opt2.repack-nonPC.pdb ReadConformPDB T0272.try12-opt2.repack-nonPC.pdb ReadConformPDB T0272.try13-opt2.repack-nonPC.pdb # ReadConformPDB T0272.try14-opt2.repack-nonPC.pdb ReadConformPDB T0272.try15-opt2.repack-nonPC.pdb ReadConformPDB T0272.try16-opt2.repack-nonPC.pdb ReadConformPDB T0272.try17-opt2.repack-nonPC.pdb # ReadConformPDB T0272.try18-opt2.repack-nonPC.pdb # ReadConformPDB T0272.try19-opt2.repack-nonPC.pdb ReadConformPDB T0272.try20-opt2.repack-nonPC.pdb ReadConformPDB T0272.try5-opt2.repack-nonPC.pdb ReadConformPDB T0272.try6-opt2.repack-nonPC.pdb ReadConformPDB T0272.try7-opt2.repack-nonPC.pdb ReadConformPDB T0272.try8-opt2.repack-nonPC.pdb ReadConformPDB T0272.try9-opt2.repack-nonPC.pdb ReadConformPDB T0272.try1-opt1-scwrl.pdb.gz ReadConformPDB T0272.try1-opt1.pdb.gz ReadConformPDB T0272.try1-opt2.pdb.gz ReadConformPDB T0272.try1-opt2.repack-nonPC.pdb.gz ReadConformPDB T0272.try10-opt1.pdb.gz ReadConformPDB T0272.try10-opt2.pdb.gz ReadConformPDB T0272.try11-opt1.pdb.gz ReadConformPDB T0272.try11-opt2.pdb.gz ReadConformPDB T0272.try12-opt1-scwrl.pdb.gz ReadConformPDB T0272.try12-opt1.pdb.gz ReadConformPDB T0272.try12-opt2.pdb.gz ReadConformPDB T0272.try13-opt1.pdb.gz ReadConformPDB T0272.try13-opt2.pdb.gz # ReadConformPDB T0272.try14-opt1.pdb.gz # ReadConformPDB T0272.try14-opt2.pdb.gz ReadConformPDB T0272.try15-opt1-scwrl.pdb.gz ReadConformPDB T0272.try15-opt1.pdb.gz ReadConformPDB T0272.try15-opt2.pdb.gz ReadConformPDB T0272.try16-opt1-scwrl.pdb.gz ReadConformPDB T0272.try16-opt1.pdb.gz ReadConformPDB T0272.try16-opt2.pdb.gz ReadConformPDB T0272.try17-opt1-scwrl.pdb.gz ReadConformPDB T0272.try17-opt1.pdb.gz ReadConformPDB T0272.try17-opt2.pdb.gz # ReadConformPDB T0272.try18-opt1-scwrl.pdb.gz # ReadConformPDB T0272.try18-opt1.pdb.gz # ReadConformPDB T0272.try18-opt2.pdb.gz # ReadConformPDB T0272.try19-opt1-scwrl.pdb.gz # ReadConformPDB T0272.try19-opt1.pdb.gz # ReadConformPDB T0272.try19-opt2.pdb.gz ReadConformPDB T0272.try2-opt1-scwrl.pdb.gz ReadConformPDB T0272.try2-opt1.pdb.gz ReadConformPDB T0272.try20-opt1-scwrl.pdb.gz ReadConformPDB T0272.try20-opt1.pdb.gz ReadConformPDB T0272.try20-opt2.pdb.gz ReadConformPDB T0272.try3-opt1-scwrl.pdb.gz ReadConformPDB T0272.try3-opt1.pdb.gz ReadConformPDB T0272.try3-opt2.pdb.gz ReadConformPDB T0272.try3-opt2.repack-nonPC.pdb.gz ReadConformPDB T0272.try4-opt1-scwrl.pdb.gz ReadConformPDB T0272.try4-opt1.pdb.gz ReadConformPDB T0272.try5-opt1-scwrl.pdb.gz ReadConformPDB T0272.try5-opt1.pdb.gz ReadConformPDB T0272.try5-opt2.pdb.gz ReadConformPDB T0272.try6-opt1-scwrl.pdb.gz ReadConformPDB T0272.try6-opt1.pdb.gz ReadConformPDB T0272.try6-opt2.pdb.gz ReadConformPDB T0272.try7-opt1-scwrl.pdb.gz ReadConformPDB T0272.try7-opt1.pdb.gz ReadConformPDB T0272.try7-opt2.gromacs.pdb.gz ReadConformPDB T0272.try7-opt2.pdb.gz ReadConformPDB T0272.try8-opt1-scwrl.pdb.gz ReadConformPDB T0272.try8-opt1.pdb.gz ReadConformPDB T0272.try8-opt2.pdb.gz ReadConformPDB T0272.try9-opt1-scwrl.pdb.gz ReadConformPDB T0272.try9-opt1.pdb.gz ReadConformPDB T0272.try9-opt2.pdb.gz ReadConformPDB robetta-model1.pdb.gz ReadConformPDB robetta-model10.pdb.gz ReadConformPDB robetta-model2.pdb.gz ReadConformPDB robetta-model3.pdb.gz ReadConformPDB robetta-model4.pdb.gz ReadConformPDB robetta-model5.pdb.gz ReadConformPDB robetta-model6.pdb.gz ReadConformPDB robetta-model7.pdb.gz ReadConformPDB robetta-model8.pdb.gz ReadConformPDB robetta-model9.pdb.gz 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 T0272.t2k.many.frag ReadFragmentAlignment T0272.t04.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 5 \ CrossOver 3 \ CrossAndInsert 5 \ TwoFragment 5 \ InsertSpecificFragment 20 \ ReduceBreak 5 \ MoveGap 5 \ HealGap 5 \ CloseGap 5 \ ReduceConstraint 5 \ ReduceClash 5 \ OptSegment 1 \ OptSubtree 1 \ InsertSSBond 0 \ ImproveSSBond 0 OptConform pool_size 20 num_gen 20 gen_size 100 \ super_iter 4 super_num_gen 60 \ scwrl_each use_all keep_all NameConform T0272.try21-opt1 PrintConformPDB T0272.try21-opt1.pdb SCWRLConform NameConform T0272.try21-opt1-scwrl PrintConformPDB T0272.try21-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 40 gen_size 100 \ super_iter 2 super_num_gen 200 use_all NameConform T0272.try21-opt2 PrintConformPDB T0272.try21-opt2.pdb # PrintConformHbonds try21-opt2.all-hbonds # PrintConformHbonds nonhelix backbone try21-opt2.beta-hbonds PrintConformSheets try21-opt2.sheets PrintConformHelices try21-opt2.helices PrintConstraints all try21-opt2.constraints # PrintConformBreaks try21-opt2.breaks CostConform Time quit