Assessing Data Quality

Why

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.

How

In Phenix the phenix.xtriage program is used to analyze data to assess quality and detect possible problems. For most uses the program only needs to be given a reflection file containing the data set you wish to analyze. Running phenix.xtriage will generate information about the data set, which are best viewed in the GUI as graphs and tables. An overall assessment of the data is given in the first section of the output.

How to use the phenix.xtriage GUI: Click here

Common issues

• Interpetation of twinning results: there are two parts to testing for twinning; whether the overall intensity statistics look normal, and then tests for specific twinning operations. Both of these kinds of tests need to indicate twinning for the data set to be considered twinned. In some cases the tests of specific twinning operations might return a high twin fraction but the overall intensity statistics look normal. This should not be interepreted as twinning, rather, more likely, a missed symmetry element (phenix.xtriage might indeed suggest a higher symmetry).

Related programs and Documentation

• phenix.plan_sad_experiment: This tool (available in the GUI) allows you to plan your SAD data collection strategy by estimating the anomalous signal and the probability of solving your structure by SAD based on the anomalously-scattering atoms, the wavelength, the size of your molecule, and the overall I/sigI for your dataset.
• phenix.anomalous_signal: This tool is like phenix.plan_sad_experiment except that it uses your measured data to give much more accurate estimates. It uses your scaled data and two half-dataset scaled datasets from your data that can be created with phenix.scale_and_merge to give an estimate of the anomalous signal in your data and the probability of solving your structure by SAD, taking into account the number of sites in the substructure.
• phenix.data_viewer: This GUI program allows you to visualize reciprocal space data either in 3-dimensions or 2-dimensions. This can be very useful for detecting systematic problems with data completeness (e.g. missing cones, wedges).
• phenix.explore_metric_symmetry: This program allows you to test whether your crystal lattice is consistent with other lattices/symmetries. It also can test whether two lattices are related. (Command line only).
• Using unmerged data in Phenix: Unmerged data can be analyzed in Phenix to provide useful information, in particular the new CC1/2 and CC* statistics. The program phenix.merging_statistics can be used to calculate these and a number of other statistics. Additionally the program phenix.scale_and_merge can scale unmerged data for you.

Phenix reference manual for phenix.xtriage