TakeTwo: an indexing algorithm suited to still images with known crystal parameters.

Helen Mary Ginn,Helen Mary Ginn,Helen Mary Ginn,Henrike Mueller-Werkmeister,Philip Roedig,Oliver P Ernst,Oliver P Ernst,Oliver P Ernst,R J Dwayne Miller,R J Dwayne Miller,R J Dwayne Miller,David Ian Stuart,David Ian Stuart,David Ian Stuart,Gwyndaf Evans,Anling Kuo,Anling Kuo,Anling Kuo,Nicholas K Sauter,Alke Meents

doi:10.1107/s2059798316010706

Abstract

The indexing methods currently used for serial femtosecond crystallography were originally developed for experiments in which crystals are rotated in the X-ray beam, providing significant three-dimensional information. On the other hand, shots from both X-ray free-electron lasers and serial synchrotron crystallography experiments are still images, in which the few three-dimensional data available arise only from the curvature of the Ewald sphere. Traditional synchrotron crystallography methods are thus less well suited to still image data processing. Here, a new indexing method is presented with the aim of maximizing information use from a still image given the known unit-cell dimensions and space group. Efficacy for cubic, hexagonal and orthorhombic space groups is shown, and for those showing some evidence of diffraction the indexing rate ranged from 90% (hexagonal space group) to 151% (cubic space group). Here, the indexing rate refers to the number of lattices indexed per image.

Highlights

Indexing, or deducing the specimen orientation from crystalline diffraction patterns, can potentially be performed with high accuracy and precision owing to the integral nature of the Miller indices at which Bragg reflections are located
The indexing methods currently used for serial femtosecond crystallography were originally developed for experiments in which crystals are rotated in the X-ray beam, providing significant three-dimensional information
We have found that in cases where only a small number of images are available, or the unit cell is large enough to obscure the low-resolution rings or prevent adequate separation of rings, a pseudo-powder pattern can still be generated by considering the projected three-dimensional vectors between spots on the Ewald sphere

Summary

Introduction

Deducing the specimen orientation from crystalline diffraction patterns, can potentially be performed with high accuracy and precision owing to the integral nature of the Miller indices at which Bragg reflections are located. Indexing algorithms implemented in programs such as XDS (Kabsch, 1993), iMosflm (Powell et al, 2013), DENZO (Otwinowski & Minor, 2006), LABELIT (Sauter et al, 2004) and DIALS (Gildea et al, 2014) are well established for data-collection strategies that involve crystal rotation, which are typically employed at synchrotron sources. For data collected at X-ray free-electron laser (XFEL) sources, where each image represents diffraction from a separate nonrotating specimen, the measure of success is less well defined. The indexing rate is defined as the percentage of hits for which crystal orientations can be determined.

Methods

Results

Conclusion