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 tryC9.costfcn Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms // Include T0197.t2k.undertaker-align.under // ReadFragmentAlignment NOFILTER T0197.t2k-2track-undertaker.a2m ReadFragmentAlignment NOFILTER SCWRL 1d8iA/1d8iA-T0197-hand1.a2m ## TryAllAlign shrink 0 min_keep_length 1 ## NameConform T0197.tryC9-al1 InfilePrefix 1d8iA/ include read-alignments-scwrl.under ## TryAllAlign shrink 0.4 min_keep_length 1 cumulative ## NameConform T0197.tryC9-al2 ## TryAllAlign shrink 0.2 min_keep_length 1 ## NameConform T0197.tryC9-al1 ## TryAllAlign shrink 0.2 min_keep_length 1 cumulative ## NameConform T0197.tryC9-al2 InfilePrefix // SCWRL keyword omitted from all-align, because SCWRL // was taking too long on some alignments. ReadFragmentAlignment NOFILTER all-align.a2m Time # ReportCost tryC9.rdb ## TryAllAlign shrink 0. min_keep_length 1 ## NameConform T0197.tryC9-al3 ## TryAllAlign shrink 0. min_keep_length 1 cumulative ## NameConform T0197.tryC9-al4 ## TryAllAlign shrink 0.3 min_keep_length 1 ## NameConform T0197.tryC9-al5 ## TryAllAlign shrink 0.3 min_keep_length 1 cumulative ## NameConform T0197.tryC9-al6 ## TryAllAlign shrink 0.1 min_keep_length 2 ## NameConform T0197.tryC9-al7 ## TryAllAlign shrink 0.1 min_keep_length 2 cumulative ## NameConform T0197.tryC9-al8 InfilePrefix decoys/ ReadConformPDB T0197.tryC8-opt1.pdb NameConform tryC8-tryC9 ReadConformPDB T0197.tryC7-opt2.pdb NameConform tryC7-tryC9 ReadConformPDB T0197.tryC7-opt2.repack-nonPC.pdb NameConform tryC7-repack-tryC9 ReadConformPDB T0197.tryC6-opt2.pdb NameConform tryC6-tryC9 ReadConformPDB T0197.tryC4-opt2.pdb NameConform tryC4-tryC9 ReadConformPDB T0197.tryC5-opt1.pdb NameConform tryC5-tryC9 # some old models to pick up helix conformations: ReadConformPDB tryB17-opt1.pdb NameConform tryB17-tryC9 ReadConformPDB tryB15-opt2.pdb NameConform tryB15-tryC9 ReadConformPDB tryB16-opt2.pdb NameConform tryB16-tryC9 ReadConformPDB tryA14-opt2.pdb NameConform tryA14-tryC9 ReadConformPDB tryA18-opt2.pdb NameConform tryA18-tryC9 ReadConformPDB try3-opt2.pdb NameConform try3-tryC9 ReadConformPDB try2-opt2.pdb NameConform try2-tryC9 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 0.5 \ ClashingRotamer 0.5 \ ClusteredRotamer 0.5 \ InsertFragment 5 \ CrossOver 15 \ CrossAndInsert 10 \ TwoFragment 1 \ InsertSpecificFragment 5 \ ReduceBreak 5 \ HealGap 5 \ CloseGap 2 \ ReduceConstraint 5 \ ReduceClash 5 \ JiggleSegment 0.2 \ JiggleSubtree 0.2 \ OptSegment 2 \ OptSubtree 2 \ OptAllSegments 1 \ TweakHbondSegment 1 \ TweakHbondSubtree 1 \ TweakPhiSegment 1 \ TweakPhiSubtree 1 \ TweakPsiSegment 1 \ TweakPsiSubtree 1 \ TweakPsiPhiSegment 1 \ TweakPsiPhiSubtree 1 \ InsertSSBond 0 \ ImproveSSBond 0 # SCWRLConform # NameConform T0197.tryC9 OptConform pool_size 20 num_gen 25 gen_size 100 \ super_iter 4 super_num_gen 100 \ use_all keep_all # scwrl_each NameConform T0197.tryC9-opt1 PrintConformPDB T0197.tryC9-opt1.pdb SCWRLConform NameConform T0197.tryC9-opt1-scwrl PrintConformPDB T0197.tryC9-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 \ TweakPsiPhiSegment 1 \ TweakPsiPhiSubtree 1 CostConform OptConform pool_size 50 num_gen 50 gen_size 100 \ super_iter 2 super_num_gen 200 use_all NameConform T0197.tryC9-opt2 PrintConformPDB T0197.tryC9-opt2.pdb PrintConformSheets tryC9-opt2.sheets PrintConstraints all tryC9-opt2.constraints PrintConformBreaks tryC9-opt2.breaks CostConform quit