SetSeed 734877 // 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 //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix /projects/compbio/experiments/protein-predict/casp7/T0ID/ # ReadTargetPDB T0ID.blank.pdb ReadTargetSeq T0ID.a2m 1 NameTarget T0ID # start with no cost function SetCost # override the cost function here: InFilePrefix include ALLCONSTRAINTS SetCost constraints 1 # Read real conformation InFilePrefix clearIDs AddID NATIVE # DO READ ReadConformPDBids SaveConformAsReal # 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 \ knot 10 clens 200 rmsd 0.0 log_rmsd 35 rmsd_ca 0.0 log_rmsd_ca 30 GDT 1 smooth_GDT 1 missing_atoms 0.2 Time InfilePrefix include servers.no-scwrl.under Time OutFilePrefix decoys/ ReportCost evaluate.constraints.rdb CostConform PrintConstraints Time quit