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The in meso in situ serial X-ray crystallography method was developed to ease the handling of small fragile crystals of membrane proteins and for rapid data collection on hundreds of microcrystals directly in the growth medium without the need for crystal harvesting. To facilitate mounting of these in situ samples on a goniometer at cryogenic or at room temperatures, two new 3D-printed holders have been developed. They provide for cubic and sponge phase sample stability in the X-ray beam and are compatible with sample-changing robots. The holders can accommodate a variety of window material types, as well as bespoke samples for diffraction screening and data collection at conventional macromolecular crystallography beamlines. They can be used for convenient post-crystallization treatments such as ligand and heavy-atom soaking. The design, assembly and application of the holders for in situ serial crystallography are described. Files for making the holders using a 3D printer are included as supporting information.

SVAT4 is a computer program for interactive visualization of three-dimensional crystal structures, including chemical bonds and magnetic moments. A wide range of functions, e.g. revealing atomic layers and polyhedral clusters, are available for further structural analysis. Atomic sizes, colors, appearance, view directions and view modes (orthographic or perspective views) are adjustable. Customized work for the visualization and analysis can be saved and then reloaded. SVAT4 provides a template to simplify the process of preparation of a new data file. SVAT4 can generate high-quality images for publication and animations for presentations. The usability of SVAT4 is broadened by a software suite for simulation and analysis of electron diffraction patterns.

This article describes new developments in the CrystalCMP software. In particular, an automatic procedure for comparison of molecular packing is presented. The key components are an automated procedure for fragment selection and the replacement of the angle calculation by root-mean-square deviation of atomic positions. The procedure was tested on a large data set taken from the Cambridge Structural Database (CSD) and the results of all the comparisons were saved as an HTML page, which is freely available on the web. The analysis of the results allowed estimation of the threshold for identification of identical packing and allowed duplicates and entries with potentially incorrect space groups to be found in the CSD.

A rational way to find the appropriate conditions to grow crystal samples for bio-crystallography is to determine the crystallization phase diagram, which allows precise control of the parameters affecting the crystal growth process. First, the nucleation is induced at supersaturated conditions close to the solubility boundary between the nucleation and metastable regions. Then, crystal growth is further achieved in the metastable zone – which is the optimal location for slow and ordered crystal expansion – by modulation of specific physical parameters. Recently, a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature–precipitant–concentration phase diagrams has been constructed. Here, it is demonstrated that a thorough knowledge of the phase diagram is vital in any crystallization experiment. The relevance of the selection of the starting position and the kinetic pathway undertaken in controlling most of the final properties of the synthesized crystals is shown. The rational crystallization optimization strategies developed and presented here allow tailoring of crystal size and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.

Exact and approximate mathematical formulas of equatorial aberration for powder diffraction data collected with an Si strip X-ray detector in continuous-scan integration mode are presented. An approximate formula is applied to treat the experimental data measured with a commercial powder diffractometer.

Total scattering measurements enable understanding of the structural disorder in crystalline materials by Fourier transformation of the total structure factor, S(Q), where Q is the magnitude of the scattering vector. In this work, the direct calculation of total scattering from a crystalline structural model is proposed. To calculate the total scattering intensity, a suitable Q-broadening function for the diffraction profile is needed because the intensity and the width depend on the optical parameters of the diffraction apparatus, such as the X-ray energy resolution and divergence, and the intrinsic parameters. X-ray total scattering measurements for CeO2 powder were performed at beamline BL04B2 of the SPring-8 synchrotron radiation facility in Japan for comparison with the calculated S(Q) under various optical conditions. The evaluated Q-broadening function was comparable to the full width at half-maximum of the Bragg peaks in the experimental total scattering pattern. The proposed calculation method correctly accounts for parameters with Q dependence such as the atomic form factor and resolution function, enables estimation of the total scattering factor, and facilitates determination of the reduced pair distribution function for both crystalline and amorphous materials.

Temperature is a ubiquitous environmental variable used to explore materials structure, properties and reactivity. This article reports a new paradigm for variable-temperature measurements that varies the temperature continuously across a sample such that temperature is measured as a function of sample position and not time. The gradient approach offers advantages over conventional variable-temperature studies, in which temperature is scanned during a series measurement, in that it improves the efficiency with which a series of temperatures can be probed and it allows the sample evolution at multiple temperatures to be measured in parallel to resolve kinetic and thermodynamic effects. Applied to treat samples at a continuum of temperatures prior to measurements at ambient temperature, the gradient approach enables parametric studies of recovered systems, eliminating temperature-dependent structural and chemical variations to simplify interpretation of the data. The implementation of spatially resolved variable-temperature measurements presented here is based on a gradient-heater design that uses a 3D-printed ceramic template to guide the variable pitch of the wire in a resistively heated wire-wound heater element. The configuration of the gradient heater was refined on the basis of thermal modelling. Applications of the gradient heater to quantify thermal-expansion behaviour, to map metastable polymorphs recovered to ambient temperature, and to monitor the time- and temperature-dependent phase evolution in a complex solid-state reaction are demonstrated.

A furnace that covers the temperature range from room temperature up to 2000 K has been designed, built and implemented on the D2AM beamline at the ESRF. The QMAX furnace is devoted to the full exploration of the reciprocal hemispace located above the sample surface. It is well suited for symmetric and asymmetric 3D reciprocal space mapping. Owing to the hemispherical design of the furnace, 3D grazing-incidence small- and wide-angle scattering and diffraction measurements are possible. Inert and reactive experiments can be performed at atmospheric pressure under controlled gas flux. It is demonstrated that the QMAX furnace allows monitoring of structural phase transitions as well as microstructural evolution at the nanoscale, such as self-organization processes, crystal growth and strain relaxation. A time-resolved in situ oxidation experiment illustrates the capability to probe the high-temperature reactivity of materials.

Hybrid photon-counting detectors are widely established at third-generation synchrotron facilities and the specifications of the Pilatus3 X CdTe were quickly recognized as highly promising in charge-density investigations. This is mainly attributable to the detection efficiency in the high-energy X-ray regime, in combination with a dynamic range and noise level that should overcome the perpetual problem of detecting strong and weak data simultaneously. These benefits, however, come at the expense of a persistent problem for high diffracted beam flux, which is particularly problematic in single-crystal diffraction of materials with strong scattering power and sharp diffraction peaks. Here, an in-depth examination of data collected on an inorganic material, FeSb2, and an organic semiconductor, rubrene, revealed systematic differences in strong intensities for different incoming beam fluxes, and the implemented detector intensity corrections were found to be inadequate. Only significant beam attenuation for the collection of strong reflections was able to circumvent this systematic error. All data were collected on a bending-magnet beamline at a third-generation synchrotron radiation facility, so undulator and wiggler beamlines and fourth-generation synchrotrons will be even more prone to this error. On the other hand, the low background now allows for an accurate measurement of very weak intensities, and it is shown that it is possible to extract structure factors of exceptional quality using standard crystallographic software for data processing (SAINT-Plus, SADABS and SORTAV), although special attention has to be paid to the estimation of the background. This study resulted in electron-density models of substantially higher accuracy and precision compared with a previous investigation, thus for the first time fulfilling the promise of photon-counting detectors for very accurate structure factor measurements.

The mechanism of formation of residual strain in crystals with a damaged surface has been studied by transmission electron microscopy in GaAs wafers ground with sandpaper. The samples showed a dislocation network located near the sample surface penetrating to a depth of a few micrometres, comparable to the size of abrasive particles used for the treatment, and no other types of defects were observed. A simple model for the formation of a compressive strain induced by the dislocation network in the damaged layer is proposed, in satisfactory agreement with the measured strain. The strain is generated by the formation of dislocation half-loops at the crystal surface, having the same component of the Burgers vectors parallel to the surface of the crystal. This is equivalent to the insertion of extra half-planes from the crystal surface to the depth of the damaged zone. This model can be generalized for other crystal structures. An approximate calculation of the strain generated from the observed dislocation distribution in the sample agrees with the proposed model and permits the conclusion that this mechanism is in general sufficient to explain the observed compressive strain, without the need to consider other types of defects.

The development of ultrashort X-ray pulse sources requires optics that keep the pulse length as short as possible. One source of pulse stretching is the penetration of the pulse into a crystal during diffraction. Another source is the inclination of the intensity front when the diffraction is asymmetric. The theory of short X-ray pulse diffraction has been well developed by many authors. As it is rather complicated, it is sometimes difficult to foresee the pulse behavior (mainly stretching) during diffraction in various crystal arrangements. In this article, a simple model is suggested that gives a qualitatively similar shape to the diffracted pulse which follows from exact theory. It allows proposal of what experimental arrangement is optimal to minimize the pulse stretching during diffraction. First, the effect of pulse stretching due to penetration into a crystal surface is studied. On the basis of this, the pulse profile change during diffraction by two crystals, either symmetric or asymmetric, is predicted.

High-quality single-crystal X-ray diffraction measurements are a prerequisite for obtaining precise and reliable structure data and electron densities. The single crystal should therefore fulfill several conditions, of which a regular defined shape is of particularly high importance for compounds consisting of heavy elements with high X-ray absorption coefficients. The absorption of X-rays passing through a 50 µm-thick LiNbO3 crystal can reduce the transmission of Mo Kα radiation by several tens of percent, which makes an absorption correction of the reflection intensities necessary. In order to reduce ambiguities concerning the shape of a crystal, used for the necessary absorption correction, a method for preparation of regularly shaped single crystals out of large samples is presented and evaluated. This method utilizes a focused ion beam to cut crystals with defined size and shape reproducibly and carefully without splintering. For evaluation, a single-crystal X-ray diffraction study using a laboratory diffractometer is presented, comparing differently prepared LiNbO3 crystals originating from the same macroscopic crystal plate. Results of the data reduction, structure refinement and electron density reconstruction indicate qualitatively similar values for all prepared crystals. Thus, the different preparation techniques have a smaller impact than expected. However, the atomic coordinates, electron densities and atomic charges are supposed to be more reliable since the focused-ion-beam-prepared crystal exhibits the smallest extinction influences. This preparation technique is especially recommended for susceptible samples, for cases where a minimal invasive preparation procedure is needed, and for the preparation of crystals from specific areas, complex material architectures and materials that cannot be prepared with common methods (breaking or grinding).

Ni-based intermetallics are promising materials for forming efficient contacts in GeSn-based Si photonic devices. However, the role that Sn might have during the Ni/GeSn solid-state reaction (SSR) is not fully understood. A comprehensive analysis focused on Sn segregation during the Ni/GeSn SSR was carried out. In situ X-ray diffraction and cross-section transmission electron microscopy measurements coupled with energy-dispersive X-ray spectrometry and electron energy-loss spectroscopy atomic mappings were performed to follow the phase sequence, Sn distribution and segregation. The results showed that, during the SSR, Sn was incorporated into the intermetallic phases. Sn segregation happened first around the grain boundaries (GBs) and then towards the surface. Sn accumulation around GBs hampered atom diffusion, delaying the growth of the Ni(GeSn) phase. Higher thermal budgets will thus be mandatory for formation of contacts in high-Sn-content photonic devices, which could be detrimental for thermal stability.

Instrumentation for time-resolved small-angle neutron scattering measurements with sub-millisecond time resolution, based on Gähler's TISANE (time-involved small-angle neutron experiments) concept, is in operation at NIST's Center for Neutron Research. This implementation of the technique includes novel electronics for synchronizing the neutron pulses from high-speed counter-rotating choppers with a periodic stimulus applied to a sample. Instrumentation details are described along with measurements demonstrating the utility of the technique for elucidating the reorientation dynamics of anisometric magnetic particles.

GIDVis is a software package based on MATLAB specialized for, but not limited to, the visualization and analysis of grazing-incidence thin-film X-ray diffraction data obtained during sample rotation around the surface normal. GIDVis allows the user to perform detector calibration, data stitching, intensity corrections, standard data evaluation (e.g. cuts and integrations along specific reciprocal-space directions), crystal phase analysis etc. To take full advantage of the measured data in the case of sample rotation, pole figures can easily be calculated from the experimental data for any value of the scattering angle covered. As an example, GIDVis is applied to phase analysis and the evaluation of the epitaxial alignment of pentacene­quinone crystallites on a single-crystalline Au(111) surface.

Serial crystallography is a powerful technique in structure determination using many small crystals at X-ray free-electron laser or synchrotron radiation facilities. The large diffraction data volumes require high-throughput software to preprocess the raw images for subsequent analysis. ClickX is a program designated for serial crystallography data preprocessing, capable of rapid data sorting for online feedback and peak-finding refinement by parameter optimization. The graphical user interface (GUI) provides convenient access to various operations such as pattern visualization, statistics plotting and parameter tuning. A batch job module is implemented to facilitate large-data-volume processing. A two-step geometry calibration for single-panel detectors is also integrated into the GUI, where the beam center and detector tilting angles are optimized using an ellipse center shifting method first, then all six parameters, including the photon energy and detector distance, are refined together using a residual minimization method. Implemented in Python, ClickX has good portability and extensibility, so that it can be installed, configured and used on any computing platform that provides a Python interface or common data file format. ClickX has been tested in online analysis at the Pohang Accelerator Laboratory X-ray Free-Electron Laser, Korea, and the Linac Coherent Light Source, USA. It has also been applied in post-experimental data analysis. The source code is available via https://github.com/LiuLab-CSRC/ClickX under a GNU General Public License.

A method for reconstructing the three-dimensional grain structure from data collected with a recently introduced laboratory-based X-ray diffraction contrast tomography system is presented. Diffraction contrast patterns are recorded in Laue-focusing geometry. The diffraction geometry exposes shape information within recorded diffraction spots. In order to yield the three-dimensional crystallographic microstructure, diffraction spots are extracted and fed into a reconstruction scheme. The scheme successively traverses and refines solution space until a reasonable reconstruction is reached. This unique reconstruction approach produces results efficiently and fast for well suited samples.

The open-source Python program PDB2INS is designed to prepare a .ins file for refinement with SHELXL [Sheldrick (2015). Acta Cryst. C71, 3–8], taking atom coordinates and other information from a Protein Data Bank (PDB)-format file. If PDB2INS is provided with a four-character PDB code, both the PDB file and the accompanying mmCIF-format reflection data file (if available) are accessed via the internet from the PDB public archive [Read et al. (2011). Structure, 19, 1395–1412] or optionally from the PDB_REDO server [Joosten, Long, Murshudov & Perrakis (2014). IUCrJ, 1, 213–220]. The SHELX-format .ins (refinement instructions and atomic coordinates) and .hkl (reflection data) files can then be generated without further user intervention, appropriate restraints etc. being added automatically. PDB2INS was tested on the 23 974 X-ray structures deposited in the PDB between 2008 and 2018 that included reflection data to 1.7 Å or better resolution in a recognizable format. After creating the two input files for SHELXL without user intervention, ten cycles of conjugate-gradient least-squares refinement were performed. For 96% of these structures PDB2INS and SHELXL completed successfully without error messages.

The room-temperature experiment has been revisited for macromolecular crystallography. Despite being limited by radiation damage, such experiments reveal structural differences depending on temperature, and it is expected that they will be able to probe structures that are physiologically alive. For such experiments, the humid-air and glue-coating (HAG) method for humidity-controlled experiments is proposed. The HAG method improves the stability of most crystals in capillary-free experiments and is applicable at both cryogenic and ambient temperatures. To expand the thermal versatility of the HAG method, a new humidifier and a protein-crystal-handling workbench have been developed. The devices provide temperatures down to 4°C and successfully maintain growth at that temperature of bovine cytochrome c oxidase crystals, which are highly sensitive to temperature variation. Hence, the humidifier and protein-crystal-handling workbench have proved useful for temperature-sensitive samples and will help reveal temperature-dependent variations in protein structures.

Obtaining crystals and solving the phase problem remain major hurdles encountered by bio-crystallographers in their race to obtain new high-quality structures. Both issues can be overcome by the crystallophore, Tb-Xo4, a lanthanide-based molecular complex with unique nucleating and phasing properties. This article presents examples of new crystallization conditions induced by the presence of Tb-Xo4. These new crystalline forms bypass crystal defects often encountered by crystallographers, such as low-resolution diffracting samples or crystals with twinning. Thanks to Tb-Xo4's high phasing power, the structure determination process is greatly facilitated and can be extended to serial crystallography approaches.

Nanoporous anodic aluminium oxide (AAO) membranes are promising host systems for confinement of condensed matter. Characterizing their structure and composition is thus of primary importance for studying the behavior of confined objects. Here a novel methodology to extract quantitative information on the structure and composition of well defined AAO membranes by combining small-angle neutron scattering (SANS) measurements and scanning electron microscopy (SEM) imaging is reported. In particular, (i) information about the pore hexagonal arrangement is extracted from SEM analysis, (ii) the best SANS experimental conditions to perform reliable measurements are determined and (iii) a detailed fitting method is proposed, in which the probed length in the fitting model is a critical parameter related to the longitudinal pore ordering. Finally, to validate this strategy, it is applied to characterize AAOs prepared under different conditions and it is shown that the experimental SANS data can be fully reproduced by a core/shell model, indicating the existence of a contaminated shell. This original approach, based on a detailed and complete description of the SANS data, can be applied to a variety of confining media and will allow the further investigation of condensed matter under confinement.

Rotation is a core crystallographic operation. Two sets of Cartesian coordinates of each point of a rotated object, those before and after rotation, are linearly related, and the coefficients of these linear combinations can be represented in matrix form. This 3 × 3 matrix is unique for all points and thus describes unambiguously a particular rotation. However, its nine elements are mutually dependent and are not interpretable in a straightforward way. To describe rotations by independent and comprehensible parameters, crystallographic software usually refers to Euler or to polar angles. In crystallography and cryo-electron microscopy, there exists a large choice of conventions, making direct comparison of rotation parameters difficult and sometimes confusing. The program py_convrot, written in Python, is a converter of parameters describing rotations. In particular, it deals with all possible choices of polar angles and with all kinds of Euler angles, including all choices of rotation axes and rotation directions. Using a menu, a user can build their own rotation parameterization; its action can be viewed with an interactive graphical tool, Demo. The tables in this article and the extended help pages of the program describe details of these parameterizations and the decomposition of rotation matrices into all types of parameters. The program allows orthogonalization conventions and symmetry operations to be taken into account. This makes the program and its supporting materials both an illustrative teaching material, especially for non-specialists in mathematics and computing, and a tool for practical use.

The Python programming language, combined with the numerical computing library NumPy and the scientific computing library SciPy, has become the de facto standard for scientific computing in a variety of fields. This popularity is mainly due to the ease with which a Python program can be written and executed (easy syntax, dynamical typing, no compilation etc.), coupled with the existence of a large number of specialized third-party libraries that aim to lift all the limitations of the raw Python language. NumPy introduces vector programming, improving execution speeds, whereas SciPy brings a wealth of highly optimized and reliable scientific functions. There are cases, however, where vector programming alone is not sufficient to reach optimal performance. This issue is addressed with dedicated compilers that aim to translate Python code into native and statically typed code with support for the multi-core architectures of modern processors. In the present article it is shown how these approaches can be efficiently used to tackle different problems, with increasing complexity, that are relevant to crystallography: the 2D Laue function, scattering from a strained 2D crystal, scattering from 3D nanocrystals and, finally, diffraction from films and multilayers. For each case, detailed implementations and explanations of the functioning of the algorithms are provided. Different Python compilers (namely NumExpr, Numba, Pythran and Cython) are used to improve performance and are benchmarked against state-of-the-art NumPy implementations. All examples are also provided as commented and didactic Python (Jupyter) notebooks that can be used as starting points for crystallographers curious to enter the Python ecosystem or wishing to accelerate their existing codes.

Bone crystallite chemistry and structure change during bone maturation. However, these properties of bone can also be affected by limited uptake of the chemical constituents of the mineral by the animal. This makes probing the effect of bone-mineralization-related diseases a complicated task. Here it is shown that the combination of vibrational spectroscopy with two-dimensional X-ray diffraction can provide unparalleled information on the changes in bone chemistry and structure associated with different bone pathologies (phosphate deficiency) and/or health conditions (pregnancy, lactation). Using a synergistic analytical approach, it was possible to trace the effect that changes in the remodelling regime have on the bone mineral chemistry and structure in normal and mineral-deficient (hypophosphatemic) mice. The results indicate that hypophosphatemic mice have increased bone remodelling, increased carbonate content and decreased crystallinity of the bone mineral, as well as increased misalignment of crystallites within the bone tissue. Pregnant and lactating mice that are normal and hypophosphatemic showed changes in the chemistry and misalignment of the apatite crystals that can be related to changes in remodelling rates associated with different calcium demand during pregnancy and lactation.

The examination of anisotropic nanostructures, such as wires, platelets or spikes, inside a transmission electron microscope is normally performed only in plan view. However, intrinsic defects such as growth twin interfaces could occasionally be concealed from direct observation for geometric reasons, leading to superposition. This article presents the shadow-focused ion-beam technique to prepare multiple electron-beam-transparent cross-section specimens of ZnO nanospikes, via a procedure which could be readily extended to other anisotropic structures. In contrast with plan-view data of the same nanospikes, here the viewing direction allows the examination of defects without superposition. By this method, the coexistence of two twin configurations inside the wurtzite-type structure is observed, namely [2 {overline 1} {overline 1} 0]^{ m W}/(0 1 {overline 1} 1) and [2 {overline 1} {overline 1} 0]^{ m W}/(0 1 {overline 1} 3), which were not identified during the plan-view observations owing to superposition of the domains. The defect arrangement could be the result of coalescence twinning of crystalline nuclei formed on the partially molten Zn substrate during the flame-transport synthesis. Three-dimensional defect models of the twin interface structures have been derived and are correlated with the plan-view investigations by simulation.

The Inorganic Crystal Structure Database (ICSD) is the world's largest database of fully evaluated and published crystal structure data, mostly obtained from experimental results. However, the purely experimental approach is no longer the only route to discover new compounds and structures. In the past few decades, numerous computational methods for simulating and predicting structures of inorganic solids have emerged, creating large numbers of theoretical crystal data. In order to take account of these new developments the scope of the ICSD was extended in 2017 to include theoretical structures which are published in peer-reviewed journals. Each theoretical structure has been carefully evaluated, and the resulting CIF has been extended and standardized. Furthermore, a first classification of theoretical data in the ICSD is presented, including additional categories used for comparison of experimental and theoretical information.

Cryocooling for macromolecular crystallography is usually performed via plunging the crystal into a liquid cryogen or placing the crystal in a cold gas stream. These two approaches are compared here for the case of nitro­gen cooling. The results show that gas stream cooling, which typically cools the crystal more slowly, yields lower mosaicity and, in some cases, a stronger anomalous signal relative to rapid plunge cooling. During plunging, moving the crystal slowly through the cold gas layer above the liquid surface can produce mosaicity similar to gas stream cooling. Annealing plunge cooled crystals by warming and recooling in the gas stream allows the mosaicity and anomalous signal to recover. For tetragonal thermolysin, the observed effects are less pronounced when the cryosolvent has smaller thermal contraction, under which conditions the protein structures from plunge cooled and gas stream cooled crystals are very similar. Finally, this work also demonstrates that the resolution dependence of the reflecting range is correlated with the cooling method, suggesting it may be a useful tool for discerning whether crystals are cooled too rapidly. The results support previous studies suggesting that slower cooling methods are less deleterious to crystal order, as long as ice formation is prevented and dehydration is limited.

Single-crystal elastic constants have been derived by lattice strain measurements using neutron diffraction on polycrystalline Ti-6Al-4V, Ti-6Al-2Sn-4Zr-6Mo and Ti-3Al-8V-6Cr-4Zr-4Mo alloy samples. A variety of model approximations for the grain-to-grain interactions, namely approaches by Voigt, Reuss, Hill, Kroener, de Wit and Matthies, including texture weightings, have been applied and compared. A load-transfer approach for multiphase alloys was also implemented and the results are compared with single-phase data. For the materials under investigation, the results for multiphase alloys agree well with the results for single-phase materials in the corresponding phases. In this respect, all eight elastic constants in the dual-phase Ti-6Al-2Sn-4Zr-6Mo alloy have been derived for the first time.

Neutron spin-echo spectrometers with a position-sensitive detector and operating with extended time-of-flight-tagged wavelength frames are able to collect a comprehensive set of data covering a large range of wavevector and Fourier time space with only a few instrumental settings in a quasi-continuous way. Extracting all the information contained in the raw data and mapping them to a suitable physical space in the most efficient way is a challenge. This article reports algorithms employed in dedicated software, DrSpine (data reduction for spin echo), that achieves this goal and yields reliable representations of the intermediate scattering function S(Q, t) independent of the selected `binning'.

The neutron powder diffractometer POWGEN at the Spallation Neutron Source has recently (2017–2018) undergone an upgrade which resulted in an increased detector complement along with a full overhaul of the structural design of the instrument. The current instrument has a solid angular coverage of 1.2 steradians and maintains the original third-generation concept, providing a single-histogram data set over a wide d-spacing range and high resolution to access large unit cells, detailed structural refinements and in situ/operando measurements.

The section of the Bilbao Crystallographic Server (http://www.cryst.ehu.es) dedicated to subperiodic groups includes a new tool called LSITESYM for the study of materials with layer and multilayer symmetry. This new program, based on the site-symmetry approach, establishes the symmetry relations between localized and extended crystal states using representations of layer groups. The efficiency and utility of the program LSITESYM is demonstrated by illustrative examples, which include the analysis of phonon symmetry in Aurivillius compounds and in van der Waals layered crystals MoS2 and WS2.

DatView is a new graphical user interface (GUI) for plotting parameters to explore correlations, identify outliers and export subsets of data. It was designed to simplify and expedite analysis of very large unmerged serial femtosecond crystallography (SFX) data sets composed of indexing results from hundreds of thousands of microcrystal diffraction patterns. However, DatView works with any tabulated data, offering its functionality to many applications outside serial crystallography. In DatView's user-friendly GUI, selections are drawn onto plots and synchronized across all other plots, so correlations between multiple parameters in large multi-parameter data sets can be rapidly identified. It also includes an item viewer for displaying images in the current selection alongside the associated metadata. For serial crystallography data processed by indexamajig from CrystFEL [White, Kirian, Martin, Aquila, Nass, Barty & Chapman (2012). J. Appl. Cryst. 45, 335–341], DatView generates a table of parameters and metadata from stream files and, optionally, the associated HDF5 files. By combining the functionality of several commonly needed tools for SFX in a single GUI that operates on tabulated data, the time needed to load and calculate statistics from large data sets is reduced. This paper describes how DatView facilitates (i) efficient feedback during data collection by examining trends in time, sample position or any parameter, (ii) determination of optimal indexing and integration parameters via the comparison mode, (iii) identification of systematic errors in unmerged SFX data sets, and (iv) sorting and highly flexible data filtering (plot selections, Boolean filters and more), including direct export of subset CrystFEL stream files for further processing.

Bragg intensities can be used to analyse crystal size distributions in a method called FXD-CSD, which is based on the fast measurement of many Bragg spots using two-dimensional detectors. This work presents the Python-based software and its graphical user interface FXD-CSD-GUI. The GUI enables user-friendly data handling and processing and provides both graphical and numerical crystal size distribution results.

A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A2A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump–probe techniques.

X-ray reflectivity (XRR) is a powerful and popular scattering technique that can give valuable insight into the growth behavior of thin films. This study shows how a simple artificial neural network model can be used to determine the thickness, roughness and density of thin films of different organic semiconductors [diindenoperylene, copper(II) phthalocyanine and α-sexithiophene] on silica from their XRR data with millisecond computation time and with minimal user input or a priori knowledge. For a large experimental data set of 372 XRR curves, it is shown that a simple fully connected model can provide good results with a mean absolute percentage error of 8–18% when compared with the results obtained by a genetic least mean squares fit using the classical Parratt formalism. Furthermore, current drawbacks and prospects for improvement are discussed.

Serial crystallography, at both synchrotron and X-ray free-electron laser light sources, is becoming increasingly popular. However, the tools in the majority of crystallization laboratories are focused on producing large single crystals by vapour diffusion that fit the cryo-cooled paradigm of modern synchrotron crystallography. This paper presents several case studies and some ideas and strategies on how to perform the conversion from a single crystal grown by vapour diffusion to the many thousands of micro-crystals required for modern serial crystallography grown by batch crystallization. These case studies aim to show (i) how vapour diffusion conditions can be converted into batch by optimizing the length of time crystals take to appear; (ii) how an understanding of the crystallization phase diagram can act as a guide when designing batch crystallization protocols; and (iii) an accessible methodology when attempting to scale batch conditions to larger volumes. These methods are needed to minimize the sample preparation gap between standard rotation crystallography and dedicated serial laboratories, ultimately making serial crystallography more accessible to all crystallographers.

Errors in the article by Opara, Martiel, Arnold, Braun, Stahlberg, Makita, David & Padeste [J. Appl. Cryst. (2017), 50, 909–918] are corrected.

The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.

It is shown that it is possible to perform combined X-ray and neutron single-crystal studies in the same diamond anvil cell (DAC). A modified Merrill–Bassett DAC equipped with an inflatable membrane filled with He gas has been developed. It can be used on laboratory X-ray and synchrotron diffractometers as well as on neutron instruments. The data processing procedures and a joint structural refinement of the high-pressure synchrotron and neutron single-crystal data are presented and discussed for the first time.

Knowledge of the appearance of texture components and fibres in pole figures, in inverse pole figures and in Euler space is fundamental for texture analysis. For cubic crystal systems, such as steels, an extensive literature exists and, for example, the book by Matthies, Vinel & Helming [Standard Distributions in Texture Analysis: Maps for the Case of Cubic Orthorhomic Symmetry, (1987), Akademie-Verlag Berlin] provides an atlas to identify texture components. For lower crystal symmetries, however, equivalent comprehensive overviews that can serve as guidance for the interpretation of experimental textures do not exist. This paper closes this gap by providing a set of scripts for the MTEX package [Bachmann, Hielscher & Schaeben (2010). Solid State Phenom. 160, 63–68] that allow the texture practitioner to compile such an atlas for a given material system, thus aiding orientation distribution function analysis also for non-cubic systems.

Silicon nanowire-based sensors find many applications in micro- and nano-electromechanical systems, thanks to their unique characteristics of flexibility and strength that emerge at the nanoscale. This work is the first study of this class of micro- and nano-fabricated silicon-based structures adopting the scanning X-ray diffraction microscopy technique for mapping the in-plane crystalline strain (∊044) and tilt of a device which includes pillars with suspended nanowires on a substrate. It is shown how the micro- and nanostructures of this new type of nanowire system are influenced by critical steps of the fabrication process, such as electron-beam lithography and deep reactive ion etching. X-ray analysis performed on the 044 reflection shows a very low level of lattice strain (<0.00025 Δd/d) but a significant degree of lattice tilt (up to 0.214°). This work imparts new insights into the crystal structure of micro- and nanomaterial-based sensors, and their relationship with critical steps of the fabrication process.

A hitherto unrecognized resolution effect in neutron Larmor diffraction (LD) is reported, resulting from small-angle neutron scattering (SANS) in the sample. Small distortions of the neutron trajectories by SANS give rise to a blurring of the Bragg angles of the order of a few hundredths of a degree, leading to a degradation of the momentum resolution. This effect is negligible for single crystals but may be significant for polycrystalline or powder samples. A procedure is presented to correct the LD data for the parasitic SANS. The latter is accurately determined by the SESANS technique (spin–echo small-angle neutron scattering), which is readily available on Larmor diffractometers. The analysis technique is demonstrated on LD and SESANS data from α-Fe2O3 powder samples. The resulting d-spacing range agrees with experimental data from high-resolution synchrotron radiation powder diffraction on the same sample.

The microstructures of six stacking-faulted industrially produced cobalt- and aluminium-bearing nickel layered double hydroxide (LDH) samples that are used as precursors for Li(Ni1−x−yCoxAly)O2 battery materials were investigated. Shifts from the brucite-type (AγB)□(AγB)□ stacking pattern to the CdCl2-type (AγB)□(CβA)□(BαC)□ and the CrOOH-type (BγA)□(AβC)□(CαB)□ stacking order, as well as random intercalation of water molecules and carbonate ions, were found to be the main features of the microstructures. A recursive routine for generating and averaging supercells of stacking-faulted layered substances implemented in the TOPAS software was used to calculate diffraction patterns of the LDH phases as a function of the degree of faulting and to refine them against the measured diffraction data. The microstructures of the precursor materials were described by a model containing three parameters: transition probabilities for generating CdCl2-type and CrOOH-type faults and a transition probability for the random intercalation of water/carbonate layers. Automated series of simulations and refinements were performed, in which the transition probabilities were modified incrementally and thus the microstructures optimized by a grid search. All samples were found to exhibit the same fraction of CdCl2-type and CrOOH-type stacking faults, which indicates that they have identical Ni, Co and Al contents. Different degrees of interstratification faulting were determined, which could be correlated to different heights of intercalation-water-related mass-loss steps in the thermal analyses.