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-2191.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 ../ ReadTargetSeq T0318.a2m 1 NameTarget T0318 // Now have a random conformation---use PopConform if you don't want it. PopConform Time OutfilePrefix // include read-pdb.under # put believed-to-be-best decoy first InFilePrefix decoys/ ReadConformPDB T0318.try1-opt2.pdb InFilePrefix M1-I177/decoys/ ReadConformPDB T0318.try10-opt2.pdb Time // Don't put superimposed models into decoys/ // since that could mess up programs that find all decoy files. OutFilePrefix printAllConformPDB superpose2.pdb superpose atom N157.CA atom E158.CA atom D159.CA atom A160.CA atom A174.CA atom R175.CA atom L176.CA atom I177.CA # Can specify a set of atoms as optional arguments of printAllConformPDB # to give initial set of atoms to align. # Format: atom A7.CA atom K252.CA ... #VAL161 PHE162 LEU163 THR164 ASP165 LEU166 SER167 GLU168 SER169 VAL170 #ARG171 GLU172 THR173 ALA174 ARG175 LEU176 ILE177 Time quit