Abstract In dealing with anomalous diffraction data from proteins, the probability distribution of three-phase structure invariants provides additional information, which can be used to resolve the phase ambiguity intrinsic in single-wavelength anomalous diffraction (SAD) enabling solution of the protein structure. Based on this, direct methods have also been used in phasing multi-wavelength anomalous diffraction (MAD) data leading to better result than that from the conventional MAD phasing.