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-40pc-3157.atoms # The rotamer library need not be from the same set of chains as the TrainingAtoms. # It encodes the most probable conformations of sidechain and backbone # for each residue type. ReadRotamerLibrary dunbrack-40pc-3157.rot Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix # ReadTargetPDB T0431.blank.pdb ReadTargetSeq T0431.a2m 1 NameTarget T0431 PopConform InFilePrefix include costfcn-init.under # include MQA_init.costfcn include try4.costfcn CostConform Time // Scale the break and clashe costs down, then gradually back up again ScaleCost break 0.25 soft_clashes 0.25 Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms // Edit this to include full sets of alignments from any // strongly-predicted superfamily // InfilePrefix 1xxxX/ // include read-alignments-scwrl.under # Include T0431.t04.undertaker-align.under ReadFragmentAlignment 2iagA/T0431-2iagA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.1136e-57 ReadFragmentAlignment 2cibA/T0431-2cibA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.9618e-56 ReadFragmentAlignment 3c6gA/T0431-3c6gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.3122e-54 ReadFragmentAlignment 1zo4A/T0431-1zo4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 4.4733e-54 ReadFragmentAlignment 2hi4A/T0431-2hi4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.2520e-52 ReadFragmentAlignment 2fdvA/T0431-2fdvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 6.7958e-52 ReadFragmentAlignment 1tqnA/T0431-1tqnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.2575e-51 ReadFragmentAlignment 3b6hA/T0431-3b6hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 4.3190e-51 ReadFragmentAlignment 1x8vA/T0431-1x8vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.2565e-50 ReadFragmentAlignment 1r9oA/T0431-1r9oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.1028e-50 ReadFragmentAlignment 1h5zA/T0431-1h5zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 9.0476e-50 ReadFragmentAlignment 1jpzA/T0431-1jpzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 9.8427e-50 ReadFragmentAlignment 3b98A/T0431-3b98A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 9.9023e-50 ReadFragmentAlignment 1u13A/T0431-1u13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.1571e-49 ReadFragmentAlignment 2ve3A/T0431-2ve3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.5631e-49 ReadFragmentAlignment 1bu7A/T0431-1bu7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 4.6259e-49 ReadFragmentAlignment 2ij2A/T0431-2ij2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 6.7694e-49 ReadFragmentAlignment 1po5A/T0431-1po5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.0913e-47 ReadFragmentAlignment 1io7A/T0431-1io7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 9.2343e-46 ReadFragmentAlignment 1qmqA/T0431-1qmqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.4623e-45 # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0431.try4-al1 # Include T0431.t06.undertaker-align.under ReadFragmentAlignment 2fdvA/T0431-2fdvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.0569e-68 ReadFragmentAlignment 1tqnA/T0431-1tqnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.8664e-68 ReadFragmentAlignment 2hi4A/T0431-2hi4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.4784e-67 ReadFragmentAlignment 3b6hA/T0431-3b6hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 3.7384e-67 ReadFragmentAlignment 1x8vA/T0431-1x8vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 4.2869e-67 ReadFragmentAlignment 2ve3A/T0431-2ve3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.1726e-66 ReadFragmentAlignment 1po5A/T0431-1po5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.9718e-66 ReadFragmentAlignment 3b98A/T0431-3b98A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.7086e-66 ReadFragmentAlignment 1jpzA/T0431-1jpzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.8142e-66 ReadFragmentAlignment 3c6gA/T0431-3c6gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 7.1538e-66 ReadFragmentAlignment 2ij2A/T0431-2ij2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.2513e-65 ReadFragmentAlignment 1zo4A/T0431-1zo4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 4.1055e-65 ReadFragmentAlignment 2cibA/T0431-2cibA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 4.2764e-65 ReadFragmentAlignment 1r9oA/T0431-1r9oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.7194e-63 ReadFragmentAlignment 2iagA/T0431-2iagA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.9259e-63 ReadFragmentAlignment 1h5zA/T0431-1h5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.9175e-63 ReadFragmentAlignment 1n97A/T0431-1n97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 7.6624e-61 ReadFragmentAlignment 2uuqA/T0431-2uuqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 9.9026e-61 ReadFragmentAlignment 1t2bA/T0431-1t2bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.4063e-60 ReadFragmentAlignment 3bujA/T0431-3bujA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 4.7842e-59 # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0431.try4-al1A # Include T0431.t2k.undertaker-align.under ReadFragmentAlignment 2hi4A/T0431-2hi4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.8969e-68 ReadFragmentAlignment 1r9oA/T0431-1r9oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 9.2188e-68 ReadFragmentAlignment 3c6gA/T0431-3c6gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.2851e-66 ReadFragmentAlignment 1h5zA/T0431-1h5zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.6109e-63 ReadFragmentAlignment 2fdvA/T0431-2fdvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 9.0238e-63 ReadFragmentAlignment 2ij2A/T0431-2ij2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 5.8208e-61 ReadFragmentAlignment 2ve3A/T0431-2ve3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.5205e-60 ReadFragmentAlignment 1zo4A/T0431-1zo4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 3.2488e-60 ReadFragmentAlignment 3b6hA/T0431-3b6hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 3.1550e-59 ReadFragmentAlignment 2cibA/T0431-2cibA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.9544e-58 ReadFragmentAlignment 2iagA/T0431-2iagA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 3.3108e-58 ReadFragmentAlignment 1tqnA/T0431-1tqnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 7.1560e-58 ReadFragmentAlignment 1x8vA/T0431-1x8vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.1805e-57 ReadFragmentAlignment 1bu7A/T0431-1bu7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.2485e-57 ReadFragmentAlignment 1u13A/T0431-1u13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.2727e-57 ReadFragmentAlignment 1dt6A/T0431-1dt6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.3021e-57 ReadFragmentAlignment 3b98A/T0431-3b98A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.5298e-56 ReadFragmentAlignment 1nr6A/T0431-1nr6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.1615e-55 ReadFragmentAlignment 1jpzA/T0431-1jpzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.2601e-55 ReadFragmentAlignment 1ea1A/T0431-1ea1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 5.0647e-55 # Include T0431.undertaker-align.under ReadFragmentAlignment 2hi4A/T0431-2hi4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 6.9462e-63 ReadFragmentAlignment 3c6gA/T0431-3c6gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.1846e-62 ReadFragmentAlignment 2fdvA/T0431-2fdvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 3.6844e-62 ReadFragmentAlignment 2cibA/T0431-2cibA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 5.2865e-61 ReadFragmentAlignment 1tqnA/T0431-1tqnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 7.5664e-61 ReadFragmentAlignment 1zo4A/T0431-1zo4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.2608e-60 ReadFragmentAlignment 2iagA/T0431-2iagA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.6869e-60 ReadFragmentAlignment 3b6hA/T0431-3b6hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.7990e-60 ReadFragmentAlignment 1r9oA/T0431-1r9oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 4.3244e-60 ReadFragmentAlignment 1x8vA/T0431-1x8vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 5.4084e-60 ReadFragmentAlignment 2ve3A/T0431-2ve3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 6.1637e-60 ReadFragmentAlignment 2ij2A/T0431-2ij2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.3701e-59 ReadFragmentAlignment 3b98A/T0431-3b98A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 4.6305e-59 ReadFragmentAlignment 1h5zA/T0431-1h5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 5.7569e-59 ReadFragmentAlignment 1jpzA/T0431-1jpzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 7.1460e-59 ReadFragmentAlignment 1po5A/T0431-1po5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.0226e-57 ReadFragmentAlignment 1n97A/T0431-1n97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 2.1672e-54 ReadFragmentAlignment 1t2bA/T0431-1t2bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.3073e-51 ReadFragmentAlignment 1izoA/T0431-1izoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.0593e-50 ReadFragmentAlignment 1io7A/T0431-1io7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER force_alignment e_value 1.1217e-50 # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0431.try4-al2 # ReadFragmentAlignment NOFILTER SCWRL force_alignment all-align.a2m # If disulfides are expected to be important, read the aligment # without SCWRL, since it destroys disulfides. # Also SCWRL is *very* slow, so try to use it less on the server. ReadFragmentAlignment NOFILTER force_alignment all-align.a2m InfilePrefix Time # ReportCost try4.rdb # TryAllAlign shrink 0. min_keep_length 1 # NameConform T0431.try4-al3 # TryAllAlign shrink 0.2 min_keep_length 1 # NameConform T0431.try4-al4 # TryAllAlign shrink 0.3 min_keep_length 1 cumulative # NameConform T0431.try4-al5 # TryAllAlign shrink 0.4 min_keep_length 1 # NameConform T0431.try4-al6 # TryAllAlign shrink 0.5 min_keep_length 1 cumulative # NameConform T0431.try4-al7 # TryAllAlign shrink 0. min_keep_length 1 # NameConform T0431.try4-al8 # SCWRLConform # NameConform T0431.try4 # OutFilePrefix decoys/ # PrintConformPDB T0431.try4-init.pdb // 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 fragment_only T0431.t2k.many.frag ReadFragmentAlignment fragment_only T0431.t04.many.frag ReadFragmentAlignment fragment_only T0431.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 \ Backrub 5 \ BigBackrub 3 \ FixOmega 0.3 \ 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 3 \ ClashingRotamer 3 \ ClusteredRotamer 2 \ ReduceBreak 5 \ CloseGap 5 \ HealGap 5 \ MoveGap 5 \ ReduceConstraint 5 \ ImproveSSBond 0 \ InsertSSBond 0 \ InsertAlignment 1 \ InsertSpecificFragment 3 \ InsertFragment 5 \ TwoFragment 5 \ CrossOver 20 \ CrossAndInsert 5 \ ReduceClash 5 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0431.try4-opt1 PrintConformPDB T0431.try4-opt1.pdb SCWRLConform NameConform T0431.try4-opt1-scwrl PrintConformPDB T0431.try4-opt1-scwrl.pdb CostConform Time ScaleCost break 2 soft_clashes 2 CostConform Time InitMethodProbs \ Backrub 2 \ BigBackrub 1 \ 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 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0431.try4-opt2 PrintConformPDB T0431.try4-opt2.pdb CostConform ScaleCost break 2 soft_clashes 2 CostConform Time OptConform pool_size 40 num_gen 60 gen_size 100 \ super_iter 2 super_num_gen 300 use_all NameConform T0431.try4-opt3 PrintConformPDB T0431.try4-opt3.pdb # PrintConformHbonds try4-opt3.all-hbonds # PrintConformHbonds nonhelix backbone try4-opt3.beta-hbonds PrintConformSheets try4-opt3.sheets PrintConformHelices try4-opt3.helices PrintConstraints all try4-opt3.constraints # PrintConformBreaks try4-opt3.breaks CostConform Time quit