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 T0489.blank.pdb ReadTargetSeq T0489.a2m 1 NameTarget T0489 PopConform InFilePrefix include costfcn-init.under # include MQA_init.costfcn include try9.costfcn // Scale the break and clash costs down, then gradually back up again ScaleCost break 0.25 soft_clashes 0.25 Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms // try9 is intended to be a generic "polishing" script that // works with existing models, rather than creating new ones from // alignments // Edit this to include full sets of alignments from any // strongly-predicted superfamily InfilePrefix 1yqyA/ include read-alignments-scwrl.under InfilePrefix 1j7nA/ include read-alignments-scwrl.under InfilePrefix 1pwuA/ include read-alignments-scwrl.under InfilePrefix 1c7kA/ include read-alignments-scwrl.under InfilePrefix 1y93A/ include read-alignments-scwrl.under InfilePrefix 1rm8A/ include read-alignments-scwrl.under InfilePrefix 1dtpA/ include read-alignments-scwrl.under InfilePrefix 1hv5A/ include read-alignments-scwrl.under # Include T0489.t04.undertaker-align.under # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0489.try9-al1 # Include T0489.t06.undertaker-align.under # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0489.try9-al1A # Include T0489.t2k.undertaker-align.under # Include T0489.undertaker-align.under # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0489.try9-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 try9.rdb # TryAllAlign shrink 0. min_keep_length 1 # NameConform T0489.try9-al3 # TryAllAlign shrink 0.2 min_keep_length 1 # NameConform T0489.try9-al4 # TryAllAlign shrink 0.3 min_keep_length 1 cumulative # NameConform T0489.try9-al5 # TryAllAlign shrink 0.4 min_keep_length 1 # NameConform T0489.try9-al6 # TryAllAlign shrink 0.5 min_keep_length 1 cumulative # NameConform T0489.try9-al7 # TryAllAlign shrink 0. min_keep_length 1 # NameConform T0489.try9-al8 # SCWRLConform # NameConform T0489.try9 OutFilePrefix decoys/ # PrintConformPDB T0489.try9-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 T0489.t2k.many.frag ReadFragmentAlignment fragment_only T0489.t04.many.frag ReadFragmentAlignment fragment_only T0489.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 4.2 \ JiggleSubtree 72.2 \ JiggleSegment 68.2 \ OptSubtree 29.2 \ OptSegment 15.2 \ OptAllSegments 0.2 \ ShiftSubtree 0.2 \ ShiftSegment 0.2 \ TweakPhiSubtree 4.2 \ TweakPhiSegment 16.2 \ TweakPsiSubtree 0.2 \ TweakPsiSegment 27.2 \ TweakPsiPhiSubtree 16.2 \ TweakPsiPhiSegment 10.2 \ TweakHbondSubtree 30.2 \ TweakHbondSegment 31.2 \ TweakMultimer 0 \ TweakPeptide 7.2 \ FixOmega 18.2 \ Backrub 75.2 \ BigBackrub 32.2 \ OneRotamer 55.2 \ ClashingRotamer 19.2 \ ClusteredRotamer 32.2 \ ReduceBreak 11.2 \ CloseGap 67.2 \ HealGap 12.2 \ MoveGap 16.2 \ ReduceConstraint 29.2 \ ImproveSSBond 0 \ InsertSSBond 0 \ InsertAlignment 0.2 \ InsertSpecificFragment 5.2 \ InsertFragment 5.2 \ TwoFragment 1.2 \ CrossOver 4.2 \ DoubleCross 4.2 \ CrossAndInsert 2.2 \ ReduceClash 25.2 \ OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0489.try9-opt1 PrintConformPDB T0489.try9-opt1.pdb SCWRLConform NameConform T0489.try9-opt1-scwrl PrintConformPDB T0489.try9-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 \ DoubleCross 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 T0489.try9-opt2 PrintConformPDB T0489.try9-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 T0489.try9-opt3 PrintConformPDB T0489.try9-opt3.pdb # PrintConformHbonds try9-opt3.all-hbonds # PrintConformHbonds nonhelix backbone try9-opt3.beta-hbonds PrintConformSheets try9-opt3.sheets PrintConformHelices try9-opt3.helices PrintConstraints all try9-opt3.constraints # PrintConformBreaks try9-opt3.breaks CostConform Time quit