Experimental Phasing


One of the biggest challenges in crystallography is the phase problem. We measure amplitudes for structure factors, but cannot directly measure the phases. Unfortunately, these phases are necessary to generate the electron density of the molecules in the crystal.

Phases can be determined by experimental phasing, which relies on a few atoms in the macromolecule with known special properties, such as a large number of electrons and/or anomalous scattering. These properties are exploited to determine the location of the special atoms (substructure), and then knowledge of the substructure in one or more crystals is used to deduce phase information for the entire macromolecule. Thus, experimental phasing solves the phase problem by using the differences in amplitudes from different diffraction experiments to determine the structure factor phases. In modern crystallography, it is most common to use single or multiple anomalous diffraction experiments (SAD/MAD).


In Phenix, the primary program for performing experimental phasing is phenix.autosol. This is a comprehensive, automatic tool that performs experimental phasing with the MAD, MIR, SIR, or SAD methods. The program locates the substructure, estimates phases, performs density modification, identifies noncrystallographic symmetry, and builds and refines a preliminary model.

To run phenix.autosol, you need to provide diffraction data, typically one or more anomalous data sets, or a native data set plus one or more derivative data sets (if you are performing SIR/MIR phasing). You also need to provide the sequence of your macromolecule, and information about the anomalous scatterers and/or heavy atoms. The phenix.autosol results include a model file containing the anomalous scatterers, an MTZ file containing the experimentally determined phases, the optimized phases from density modification, and, if the maps are of sufficient quality, an atomic model.

How to use the phenix.autosol GUI: Click here

Phenix reference manual for phenix.autosol

Common issues

Related programs