[2] In diffraction or microscopy experiments, the phase part of the wave often contains valuable information on the studied specimen.
The phase problem constitutes a fundamental limitation ultimately related to the nature of measurement in quantum mechanics.
In X-ray crystallography, the diffraction data when properly assembled gives the amplitude of the 3D Fourier transform of the molecule's electron density in the unit cell.
For practical purposes, it is limited to "small molecules" and peptides because they consistently provide high-quality diffraction with very few reflections.
Multiple isomorphous replacement (MIR), where heavy atoms are inserted into structure (usually by synthesizing proteins with analogs or by soaking) A powerful solution is the multi-wavelength anomalous dispersion (MAD) method.
Since X-ray fluorescence techniques (like this one) require excitation at very specific wavelengths, it is necessary to use synchrotron radiation when using the MAD method.
In many cases, an initial set of phases are determined, and the electron density map for the diffraction pattern is calculated.
These phases are reapplied to the original amplitudes, and an improved electron density map is derived, from which the structure is corrected.