Abstract
A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink-beam X-ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit-cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink-beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi-monochromatic X-rays and with electrons the algorithm indexed more patterns than other programs tested.
Highlights
Protein crystallography is a vibrant and continually evolving field spurred by the development of new radiation sources, detectors, measurement techniques and analysis methods
The indexer presented in this paper has been developed for pink-beam serial crystallography using the full polychromatic spectrum of an undulator harmonic at a synchrotron radiation facility
Starting from known unit-cell parameters, the pinkIndexer algorithm works by mapping all possible rotations of candidate reciprocal-lattice points onto line segments in reciprocal space that correspond to Bragg peaks of unknown wavelength
Summary
Protein crystallography is a vibrant and continually evolving field spurred by the development of new radiation sources, detectors, measurement techniques and analysis methods. These include an approach due to Jacobson (1986) that requires the use of an energy-resolving position-sensitive detector; the Daresbury software suite for indexing Laue patterns (Helliwell et al, 1989; Campbell et al, 1998) and the Precognition software (Ren et al, 1999) based on searching arcs of reflections so that prominent zone axes can be identified; geometric approaches of Carr et al (1993) and Wenk et al (1997); and the LaueUtil toolkit (Kalinowski et al, 2011) which carries out a clustering analysis of possible orientations that map lattice vectors to observed peaks The latter algorithm requires measurements of a crystal at several known relative orientations and is not suited to serial crystallography. The algorithm can be employed in automated processing of serial crystallography data sets, for example using the CrystFEL sofware suite (White et al, 2012; White, 2019)
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