cctbx.xfel : a suite for processing serial crystallographic data

The cctbx.xfel suite of processing programs and tools allows fast, visual analysis of serial diffraction images from synchrotrons and XFELs. Built on DIALS and cctbx, cctbx.xfel is designed for real-time and post-experiment processing with a fully featured graphical user interface. Users can quickly identify hitrates, view diffraction patterns, analyze unit-cell isomorphism using clustering, and merge data using a metadata tagging approach that allows on-the-fly organization and visualization of processing results. This paper describes the fundamental algorithms and command-line programs used by cctbx.xfel, including the two main program dials.stills_process, which performs spot-finding, indexing, geometric refinement, and integration, and cctbx.xfel.merge, which performs scaling, post-refinement, and merging. A discussion of merging statistics is presented and newer features are described, including random sub-sampling for indexing multi-lattice hits and ΔCC _1/2 filtering to remove outliers. Finally we show a complex, heterogeneous sample containing hexagonal and monoclinic isoforms in P6₃ and P2₁. The isoforms are separated by unit cell clustering, and for each isoform we resolve a (pseudo-)merohedral indexing ambiguity.