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/T0229.try2-opt2.pdb NameTarget T0229 MakeGenericFragmentLibrary Time InFilePrefix Time ReadTemplatePDB 1ml8.pdb1 model 1 name 1ml8A ReadTemplatePDB 1ml8.pdb1 model 2 name 1ml8B ReadFragmentAlignment NOFILTER 1ml8A/1ml8A-T0229.2mer-a2m PrintMultimerPDB 2 dimer-1ml8A-try2.pdb Time