Metrology evaluation

Metrology refinement should proceed until metrology has converged, meaning there are no longer meaningful changes in panel positions. There are two useful tools for this: detector residuals and detector shifts.

Detector residuals

To see overall plots showing accuracy of the crystallographic models, take any pair of json and reflection table pickles and run cctbx.xfel.detector_residuals. For example:

cctbx.xfel.detector_residuals cspad_combined_experiments.json cspad_combined_reflections.pickle hierarchy=2

This program was used to create Figure 3. See the corresponding Jupyter notebook for more details. In addition to the plots, the overall RMSD (obs-calc) is shown.

Detector shifts

The program cspad.detector_shifts can be used to compute the magnitude of panel movements during refinement. Example:

cspad.detector_shifts cspad_combined_experiments.json cspad_combined_reflections.pickle cspad_refined_experiments_step7_level2.json cspad_refined_reflections_step7_level2.pickle

This command shows the magnitude of changes between the unrefined detector and the last step of one cycle of refinement. See especially the last table, detector shifts summary. This program was used to create Table 6.