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 decoys/T0366.try3-opt2-edit7.pdb.gz NameTarget T0366 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 1g9oA/ ReadTemplatePDB 1g9o.mmol chain A name 1g9oA ReadTemplatePDB 1g9o.mmol chain B name 1g9oB OutFilePrefix dimer/decoys/ InFilePrefix 1g9oA/ ReadFragmentAlignment NOFILTER T0366-1g9oA.dimer-a2m InFilePrefix PrintMultimerPDB 2 dimer-try3-1g9oA-take6.pdb Time