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 ReadTargetPDB dimer/decoys/Proteinshop/try5-opt2.chain1.rotate2.renum.pdb NameTarget T0284 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: // ReadTemplatePDB 1xxx.pdb1 model 1 name 1xxxA // ReadTemplatePDB 1xxx.pdb1 model 2 name 1xxxB OutFilePrefix dimer/decoys/ InFilePrefix 1mumA/ ReadFragmentAlignment NOFILTER 1mumA.dimer-a2m InFilePrefix PrintMultimerPDB 2 rotate2.pdb Time