The crystallographic phase problem is a calculation that must be done to determine the position of atoms in a protein structure, to give the relative position of each atom. This calculation is done during the Fourier transformation, allowing the production of an atomic model.
A lens would allow this issue to be removed from protein structure determination, however X-ray lenses are not great and so this issue persists.
These calculations have become simpler with advances in computing technology, allowing them to be completed faster and with less human intervention.