issue contents

Journal logoJOURNAL OF
APPLIED
CRYSTALLOGRAPHY
ISSN: 1600-5767

October 2017 issue

Highlighted illustration

Cover illustration: Schematic representations of the [beta]-hematin molecule and the formation of the constituent ferroprotoporphyrin IX dimers. [beta]-Hematin is the synthetic form of hemozoin, which is a waste by-product of the malaria parasite. Courtesy of Dilanian et al. [J. Appl. Cryst. (2017), 49, 1533-1540].

research papers


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A compact and general formula for the form factor of any polyhedron is given and its singularities are discussed, together with illustrative examples.

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The dynamical theory of X-ray diffraction has been developed for spatially restricted beams. This approach allows one to calculate rocking curves as well as reciprocal space maps for both transmitted and reflected coherent wavefields.

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This paper applies three-dimensional visualization techniques to synthetic and experimentally acquired material textures (random, cube and Goss texture components) and illustrates how three-dimensional visualization can be used to gain insight about orientation distribution functions and orientation relations. The intrinsic symmetry of the Euler orientation representations is considered in detail and it is shown that a monoclinic magnetic space group properly describes the symmetry of Euler space.

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An extensive round robin experiment between small-angle X-ray scattering laboratories has delivered a global uncertainty estimate for the measurands of a nanoparticle dispersion. Irrespective of the instrument pedigree, the distribution mean, width and volume fraction could be determined with an accuracy of 1, 10 and 10%, respectively.

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Small-angle scattering is used to reveal the buried nanostructure and to uncover structure–property relationships in all-polymer photovoltaics.

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An automated analysis approach for recognition of grain boundaries in face-centred cubic based zincblende materials from high-resolution high-angle annular dark-field scanning transmission electron microscopy images is described and its performance is tested.

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A rigorous analysis of sampling and intensity statistics for a powder diffraction experiment over a range of nanocrystallite sizes is presented.

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Lp-Search is an X-ray powder diffraction algorithm that is independent of peak position extraction and instead directly uses the observed data. It requires limited input parameters and should be useful for indexing problems where peak intensity extraction is difficult owing to peak overlap.

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A description of peak shapes, peak intensities and peak shifts from a capillary specimen has been developed for use in X-ray powder diffraction from a fundamental parameters perspective. The capillary diameter, specimen linear absorption coefficients and focal length of the X-ray beam can be refined in a Rietveld refinement sense.

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The weather parameters during crystallization solution preparation, including the ambient temperature, humidity, pressure and particulate matter in the air, can all affect protein crystallization. Among the parameters investigated in this study, humidity showed the strongest effect on lysozyme crystallization. The results suggest that the weather conditions during the preparation of a crystallization experiment should be considered as a potential factor that can influence protein crystallization.

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The Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.

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A spatially resolved texture analysis investigation of Napoleonic War era copper bolts from four identified wrecks, HMS Impregnable (completed 1786), HMS Amethyst (1799), HMS Pomone (1805) and HMS Meander (1840), is presented.

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The onset of the strain relaxation process has been studied by examination of the diffuse scattering observed on symmetrical reciprocal-space maps. It is shown that the size and shape of the diffuse scattering are closely related to the density of dislocations.

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A calibration procedure for small-angle neutron scattering (SANS) data is presented, where geometric effects are treated analytically and voxel sensitivities are calibrated with measurements of an arbitrary scatterer. This allows correction of the measured intensities with a single measurement, without the need to measure an isotropic scatterer at all used instrumental settings.

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The transformation cycle between the spherically symmetric correlation function, projected correlation function and differential cross section [\tilde{\gamma}(r), \tilde{G}(\delta) and I(q)] as implemented in SASfit is described.

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Simultaneous small-angle neutron scattering and dilatometry reveal water-adsorption-induced deformation of silica materials with hierarchical porosity along with their adsorption isotherm.

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Significant gains in the performance of the global optimization algorithm in the DASH software package have been realized using the irace automatic configuration tool and are demonstrated using over 100 powder diffraction datasets.

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Significant gains in the performance of the DASH software package have been realized using conformational information derived from the Cambridge Structural Database and are demonstrated using 51 powder diffraction data sets.

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An extended model for reconstruction of periodic multilayers from grazing-incidence X-ray and normal-incidence extreme ultraviolet reflectivity data is proposed; simulated and experimental data fits are presented.

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A formalism for dark-field X-ray microscopy is presented and validated. The coupled resolution function in direct and reciprocal space is derived and space-filling sampling approaches are described.

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A new section of computer tools devoted to the double crystallographic groups has been implemented in the Bilbao Crystallographic Server (http://www.cryst.ehu.es). The section includes databases of symmetry operations and irreducible representations of the double point and space groups and programs that compute the compatibility relations, generate relevant information related to the site-symmetry approach, and calculate band representations and elementary band representations induced from any Wyckoff position of any double space group.

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An X-ray diffraction study was conducted on a (111)-textured palladium thin film under cyclic hydrogen loading. The film structure evolution was observed and its mechanism investigated.

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A new reflection model for X-ray diffraction from mosaic crystals has been developed with which it is possible, in contrast to Zachariasen's well established model, to describe the crystal reflectivity in a spatially resolved manner. Introduced in a ray-tracing simulation, the simulations show very good agreement with measurements, because multiple reflections and their spatial effects are included.

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Intermolecular interactions in the N-(4-methyl­benzyl)­benzamide crystal are perfectly discerned using a Hirshfeld surface. A method to determine the crystal morphology from the propagation vector of the centre of mass of the molecular basis in the crystal system is outlined.

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Morphological and crystallographic anisotropy of severely deformed commercially pure aluminium is studied by conventional and three-dimensional electron backscatter diffraction. Saturation of texture, grain refinement and the formation of microstructure are discussed in the light of different microstructural coarsening mechanisms.

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The shallow incidence angles in grazing-incidence small-angle X-ray scattering (GISAXS) allow the use of a rigorous Maxwell solver in combination with the finite-element method for the reconstruction of nanometre-sized periodic surface structures.

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Serial femtosecond crystallography (SFX) at an X-ray free-electron laser enables crystllographic data to be collected from samples orders of magnitude smaller than at a synchrotron. Here SFX is used to investigate the nascent structure of β-hematin derived from nanocrystals and this is compared with the well known structure derived from macroscopic crystals of the same material.

teaching and education


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The incorrect restriction to integer values for direction indices in centred cells and the potential consequences are pointed out and corrected.

computer programs


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BioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data, including size-exclusion chromatography coupled SAXS data. The software is designed for biological data and enables creation and plotting of one-dimensional scattering profiles from two-dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and more advanced analyses such as calculation of inverse Fourier transforms.

laboratory notes


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A simple transfer device is described that enables cutting of an oriented single crystal.

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A new design of a setup for in situ laser irradiation of single crystals during an X-ray diffraction experiment is reported.

addenda and errata


crystallographers


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