James M. Parkhurst

Diffraction‐geometry refinement in the DIALS framework

A comprehensive description of the methods used within the DIALS framework for diffraction-geometry refinement using predicted reflection centroids is given. Examples of the advanced features of the software are provided.

New methods for indexing multi-lattice diffraction data

A new indexing method is presented which is capable of indexing multiple crystal lattices from narrow wedges of data. The efficacy of this method is demonstrated with both semi-synthetic multi-lattice data and real multi-lattice data recorded from microcrystals of ∼1 µm in size.

DIALS: implementation and evaluation of a new integration package

A new X-ray diffraction data-analysis package is presented with a description of the algorithms and examples of its application to biological and chemical crystallography.

dxtbx: the diffraction experiment toolbox

A Python/C++ library for reading image data and experimental geometry for X-ray diffraction experiments from arbitrary data sources is presented.

Robust background modelling in DIALS

The application of a robust generalized linear model framework for the modelling of reflection backgrounds in X-ray diffraction images is described.

Background modelling of diffraction data in the presence of ice rings

An algorithm for modelling the background of X-ray diffraction images in the presence of ice rings is presented.

AUSPEX: a graphical tool for X-ray diffraction data analysis

AUSPEX is a new software tool for the statistical analysis of single-crystal X-ray diffraction data. It can be used to identify problems in the data resulting from the experiment itself, image processing, data scaling or conversion.

Improving signal strength in serial crystallography with DIALS geometry refinement

For XFEL data, simultaneous refinement of multi-panel detector geometry with thousands of crystal models in the program DIALS improves the integrated signal quality and helps to reduce non-isomorphism

Maximum-likelihood methods in DIALS

In macromolecular crystallography, integration programs such as DIALS (Waterman et al. 2013) are used to estimate the intensities of Bragg reflections recorded on a series of X-ray diffraction images. The reflection intensities are estimated using the following procedure. A model for the shape of the reflection profile is estimated from a set of strong reflections. This model is then applied to each reflection in order to estimate the size and shape of the reflection on the detector surface and to label each pixel as either foreground or background. The intensity of each reflection is then estimated (in the case of summation integration) by summing the total counts minus the estimated background counts in the foreground region. Since the background level under the reflection peak cannot be measured directly, it is estimated from the surrounding background pixels assuming a given model.

Treatment of X-ray diffraction data at Diamond Light Source

In any experimental discipline, raw data represents the source from which all discoveries are derived. A more strict interpretation in X-ray diffraction experiments may refer to this as primary data since any pixel counts will have been manipulated (e.g. analogue to digital conversion, dark current correction, interpolation of pixels etc.); however the fundamental idea remains: this is the closest it is possible to get to the original experimental measurements.