SetSeed // Note: the training atoms are needed for patching up chain breaks // when reading in conformations. InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/ ReadTrainingAtoms monomeric-50pc.atoms ReadRotamerLibrary dunbrack-1332.rot InFilePrefix /projects/compbio/experiments/undertaker/spots/ ReadAtomType exp-pdb.types ReadClashTable exp-pdb-2191-2symm.clash SetClashDefinition exp-pdb-2191-2symm Time 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 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 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-2191-alpha.hist CreateAlphaCost alpha_prev dunbrack-2191-alpha-1.hist -1 InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix # ReadTargetPDB XXX0000.blank.pdb ReadTargetSeq XXX0000.a2m START_COL NameTarget XXX0000 PopConform # Read real conformation # Read conformation by specifying a PDB id clearIDs AddID REAL_PDB # DO READ ReadConformPDBids # ReadConformPDB XXX0000_domain.real.pdb SaveConformAsReal OutFilePrefix decoys/ # PrintConformGDT real-vs-real.gdt # quit # perfect match should be cost -1. # different components are scaled to have roughly equal weight # (roughly a difference of 1 between great models and totally wrong ones) SetRealCost real_hbond 50 real_hbond_u 50 decoy_hbond 50 decoy_hbond_u 50 \ real_NO_hbond 10 real_NO_hbond_u 10 decoy_NO_hbond 10 decoy_NO_hbond_u 10 \ clens 200 rmsd 0.0 log_rmsd 35 rmsd_ca 0.0 log_rmsd_ca 30 GDT 1 smooth_GDT 1 missing_atoms 0 # start with no cost function SetCost # override the cost function here: include COSTFCN.costfcn Time InfilePrefix decoys/ include read-pdb.under Time OutFilePrefix decoys/ ReportCost servers.mqa2.COSTFCN.rdb #MQA2 servers.mqa2.COSTFCN.mqa2 CostConform servers.mqa2.COSTFCN.mqa2 Time quit