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 T0403.blank.pdb ReadTargetSeq T0403.a2m 1 NameTarget T0403 PopConform InFilePrefix include costfcn-init.under # include MQA_init.costfcn include try9.costfcn // Scale the break and clashe costs down, then gradually back up again ScaleCost break 0.11111 soft_clashes 0.11111 Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms // Edit this to include full sets of alignments from any // strongly-predicted superfamily InfilePrefix 2fgqX/ include read-alignments-scwrl.under InfilePrefix 1hxxA/ include read-alignments-scwrl.under InFilePrefix Include T0403.t04.undertaker-align.under # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0403.try9-al1 InfilePrefix 2j1nA/ include read-alignments-scwrl.under InfilePrefix 2porA/ include read-alignments-scwrl.under InFilePrefix Include T0403.t06.undertaker-align.under # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0403.try9-al1A InfilePrefix 3prnA/ include read-alignments-scwrl.under InfilePrefix 1e54A/ include read-alignments-scwrl.under InfilePrefix 2o4vA/ include read-alignments-scwrl.under InfilePrefix 1t16A/ include read-alignments-scwrl.under InFilePrefix Include T0403.t2k.undertaker-align.under Include T0403.undertaker-align.under # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0403.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 T0403.try9-al3 # TryAllAlign shrink 0.2 min_keep_length 1 # NameConform T0403.try9-al4 # TryAllAlign shrink 0.3 min_keep_length 1 cumulative # NameConform T0403.try9-al5 # TryAllAlign shrink 0.4 min_keep_length 1 # NameConform T0403.try9-al6 # TryAllAlign shrink 0.5 min_keep_length 1 cumulative # NameConform T0403.try9-al7 # TryAllAlign shrink 0. min_keep_length 1 # NameConform T0403.try9-al8 # SCWRLConform # NameConform T0403.try9 # OutFilePrefix decoys/ # PrintConformPDB T0403.try9-init.pdb // Switch to the following (commenting out the TryAllAlign) // to polish existing models InfilePrefix decoys/ # include read-pdb.under ReadConformPDB chimera-try8-MQAC1.pdb.gz ReadConformPDB chimera-try8-MQAC2.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 fragment_only T0403.t2k.many.frag ReadFragmentAlignment fragment_only T0403.t04.many.frag ReadFragmentAlignment fragment_only T0403.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 10 \ FixOmega 0.3 \ HealPeptide 0.3 \ JiggleSubtree 0.3 \ JiggleSegment 0.3 \ OptSubtree 1 \ OptSegment 10 \ 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 1 \ ClashingRotamer 1 \ ClusteredRotamer 2 \ ReduceBreak 10 \ CloseGap 10 \ HealGap 10 \ MoveGap 2 \ ReduceConstraint 15 \ ImproveSSBond 0 \ InsertSSBond 0 \ InsertAlignment 1 \ InsertSpecificFragment 5 \ InsertFragment 5 \ TwoFragment 10 \ CrossOver 10 \ CrossAndInsert 5 \ ReduceClash 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 T0403.try9-opt1 PrintConformPDB T0403.try9-opt1.pdb SCWRLConform NameConform T0403.try9-opt1-scwrl PrintConformPDB T0403.try9-opt1-scwrl.pdb CostConform Time ScaleCost break 3 soft_clashes 3 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 T0403.try9-opt2 PrintConformPDB T0403.try9-opt2.pdb CostConform ScaleCost break 3 soft_clashes 3 CostConform Time OptConform pool_size 40 num_gen 60 gen_size 100 \ super_iter 2 super_num_gen 300 use_all NameConform T0403.try9-opt3 PrintConformPDB T0403.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