SetSeed InfilePrefix // Note: the training atoms are needed for patching up chain breaks // when reading in conformations. InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/ ReadTrainingAtoms dunbrack-2191.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 decoys/ ReadTargetPDB T0375.try2-opt2.pdb NameTarget T0375 MakeGenericFragmentLibrary Time InFilePrefix Time # If multimer is not already in pdb, but needs crystal symmetries to generate, # then fetch the "biological unit" from pdb and use the following commands: InFilePrefix 1rkd/ ReadTemplatePDB 1rkd.mmol chain A name 1rkdA ReadTemplatePDB 1rkd.mmol chain B name 1rkdB ReadFragmentAlignment NOFILTER T0375-1rkd.dimer-a2m OutFilePrefix dimer/decoys/ PrintMultimerPDB 2 dimer-1rkd.pdb Time InFilePrefix 1rkd/ ReadTemplatePDB 1rk2.mmol chain A name 1rk2A ReadTemplatePDB 1rk2.mmol chain B name 1rk2B ReadFragmentAlignment NOFILTER T0375-1rk2.4mer-a2m OutFilePrefix 4mer/decoys/ PrintMultimerPDB 2 4mer-1rkd2.pdb Time