An approach to the description of local atomic disorder (short-range order) in single crystals by the mixed-symmetry method based on Bragg scattering data is proposed, and the corresponding software is developed. In defect-containing crystals, each atom in the unit cell can be described by its own symmetry space group. The expression for the calculated structural factor includes summation over different sets of symmetry operations for different atoms. To facilitate the search for new symmetry elements, an “atomic disorder expert” was developed, which estimates the significance of tested models. It is shown that the symmetry lowering for some atoms correlates with the existence of phase transitions (in langasite family crystals) and the anisotropy of physical properties (in rare-earth dodecaborides R B 12 ).