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 T0329.a2m 1 NameTarget T0329 // Now have a random conformation---use PopConform if you don't want it. PopConform Time InFilePrefix decoys/delme/ ReadConformPDB main.pdb ReadConformPDB insert.pdb Time OutFilePrefix decoys/delme/ printAllConformPDB superpose.pdb superpose atom I205.CA atom V185.CA atom A154.CA atom Q218.CA atom N120.CA atom V226.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 ... Time quit