SetSeed InfilePrefix // Note: the training atoms are needed for patching up chain breaks // when reading in conformations. InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/ ReadTrainingAtoms monomeric-50pc.atoms ReadRotamerLibrary dunbrack-1332.rot InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/spots/ ReadAtomType pdb-name.types ReadClashTable pdb-atom-name.clash SetClashDefinition pdb-atom-name Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix ReadTargetPDB decoys/from-dimer-try4B.pdb NameTarget T0263 MakeGenericFragmentLibrary Time InFilePrefix Time AddId 1lq9A AddId 1lq9B ReadTemplatePDBIds InFilePrefix 1lq9A/ ReadFragmentAlignment NOFILTER 1lq9.2mer-a2m InFilePrefix PrintMultimerPDB 2 dimer-1lq9-try4B.pdb Time