Assessing Data Quality


The first step after data processing is analysis of the diffraction data to assess quality and detect any pathologies that might make structure solution difficult. Data quality can be quantified in terms of resolution of diffraction, anomalous signal-to-noise, and consistency with prior knowledge about diffraction from crystals.

Possible pathologies include twinning, translational non-crystallographic symmetry, anisotropy, and missed symmetry elements. For example, crystals are considered ‘twinned’ if two or more separate crystals (domains) are intergrown in such a way that they share some crystal lattice points in a symmetrical manner. And translational noncrystallographic symmetry (tNCS) occurs when two or more independent copies of a molecule or assembly have a similar orientation in the asymmetric unit of the crystal.


The phenix.xtriage program analyzes data to assess quality and detect possible problems. For most uses, the program only requires a reflection file containing the data set you wish to analyze. Running phenix.xtriage generates information about the data set, which is best viewed in the GUI as graphs and tables. The first section of the output provides an overall assessment of the data.

How to use the phenix.xtriage GUI: Click here

Phenix reference manual for phenix.xtriage

Common issues

Interpretation of twinning results: There are two parts to testing for twinning — determining whether the overall intensity statistics look normal, and testing for specific twinning operations. Both kinds of tests need to indicate twinning for the data set to be considered twinned. In some cases, the tests of specific twinning operations return a high twin fraction but the overall intensity statistics look normal; this should not be interpreted as twinning. More likely, a symmetry element is missing, and phenix.xtriage might suggest a higher symmetry.

Related programs and Documentation