Experimental Phasing


One of the biggest problems 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. 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 powerful tool that goes through the steps of anomalous substructure location, phasing, phase improvement, and initial model building. To run phenix.autosol you will 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 will also need to provide the sequence of your macromolecule, and information about the anomalous scatterers and/or heavy atoms. The results from phenix.autosol will include a PDB containing the anomalous scatterers, an MTZ file containing the experimentally determined phases, and the optimized phases from density modification, and, if the maps are of sufficient quality a PDB file with an atomic model.

How to use the phenix.autosol GUI: Click here

Common issues

Related programs

Phenix reference manual for phenix.autosol