issue contents

Journal logoJOURNAL OF
ISSN: 1600-5767

October 2009 issue

Highlighted illustration

Cover illustration: Three-dimensional reconstructed crystal (purple), loop (yellow) and solvent (transparent pink) for a native DNA sample. Courtesy of Brockhauser, Di Michiel, McGeehan, McCarthy & Ravelli [J. Appl. Cryst. (2008), 41, 1057-1066].

research papers

J. Appl. Cryst. (2009). 42, 749-757
doi: 10.1107/S0021889809024856
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The overall gain and point-spread function of an image-plate detector system can be determined online from single-crystal diffraction patterns to facilitate unbiased estimation of the true standard deviations of the observed integrated intensities of the Bragg reflections.

J. Appl. Cryst. (2009). 42, 758-767
doi: 10.1107/S0021889809030349
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Comparison of finite element analysis with high-energy X-ray diffraction measurements demonstrates the possibility of extracting the gradation of long-range strain fields in massive high-quality single crystals like silicon from the measured Bragg intensities.

J. Appl. Cryst. (2009). 42, 768-775
doi: 10.1107/S0021889809025503
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A new approach is described for indexing a powder pattern and determining the extinction group. A new figure of merit is also given.

J. Appl. Cryst. (2009). 42, 776-782
doi: 10.1107/S0021889809026636
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An X-ray diffraction measurement was performed by using a TiN thin-film specimen with [111] fibre texture, in order to see whether a profile of the 420 X-ray reflection changes or not depending on the biaxial load. The results obtained by this examination agree quantitatively with a theoretical prediction.

J. Appl. Cryst. (2009). 42, 783-792
doi: 10.1107/S0021889809025461
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Models of uniformity needed for defning statistical grain boundary density functions are discussed. It is proposed to use some models derived from an assumed metric of grain boundary space.

J. Appl. Cryst. (2009). 42, 793-797
doi: 10.1107/S0021889809023589
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The apical ligand is bonded at the sterically more crowded side of a complex, and apical bond length shows sigmoidal dependence on distortion of the coordination polyhedron.

J. Appl. Cryst. (2009). 42, 798-809
doi: 10.1107/S0021889809024376
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Cell-error effects on crystallographic data and on derived parameters are reviewed. New algorithms are presented for more efficient error handling.

J. Appl. Cryst. (2009). 42, 810-814
doi: 10.1107/S0021889809025138
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The computer program PTRY has been devised to perform X-ray structural studies of crystalline peptides when only limited diffraction data are available. It is based on a random search in the internal-coordinate space and evolutionary algorithms.

J. Appl. Cryst. (2009). 42, 815-819
doi: 10.1107/S0021889809023310
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An in situ synchrotron radiation grazing-incidence diffraction study is presented of the kinetics of the formation of nanoparticles of ZnO grown by the aqueous chemical growth technique.

J. Appl. Cryst. (2009). 42, 820-833
doi: 10.1107/S0021889809028064
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AMPLIMODES is a computer program available on the Bilbao Crystallographic Server that can perform a symmetry-mode analysis of any distorted structure of displacive type.

J. Appl. Cryst. (2009). 42, 834-845
doi: 10.1107/S0021889809023218
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This paper describes the development of efficient crystals for a Laue lens application. The theoretical study aimed to identify the crystals, either pure or two-component crystals, best suited to this application and three different materials were then characterized experimentally.

J. Appl. Cryst. (2009). 42, 846-866
doi: 10.1107/S0021889809027897
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This paper reports neutron powder diffraction studies of ammonia dihydrate up to 2 GPa, including identification of new high-pressure polymorphs and measurement of their equations of state. Data for co-existing water ice and ammonia monohydrate polymorphs are also reported.

J. Appl. Cryst. (2009). 42, 867-877
doi: 10.1107/S0021889809023541
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Extended X-ray absorption fine structure (EXAFS) data were included in simultaneously fitted experimental data for the reverse Monte Carlo refinement of local atomic structure using the public domain software RMCProfile. Structural refinements of complex perovskites demonstrated that inclusion of the EXAFS data provided the constraints necessary to recover fine details of the local atomic arrangements.

J. Appl. Cryst. (2009). 42, 878-884
doi: 10.1107/S0021889809025709
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A simplified data acquisition and analysis technique, for determining the main refractive indices and the thickness of a uniaxial anisotropic crystal cut out parallel with the optical axis by digitally processing the conoscopic interference figures, is presented.

J. Appl. Cryst. (2009). 42, 885-891
doi: 10.1107/S0021889809030921
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Experiments are described in which a direct comparison was made between a conventional sealed tube and a microfocus X-ray source with multilayer optics. They reveal the latter to be far superior for the investigation of small crystals.

J. Appl. Cryst. (2009). 42, 892-900
doi: 10.1107/S0021889809029288
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A prototype was developed to perform online purification and automatic loading of protein solutions at a small-angle X-ray scattering beamline.

J. Appl. Cryst. (2009). 42, 901-905
doi: 10.1107/S0021889809027873
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A newly developed fast mechanical X-ray chopper provides an opening time of 230 ns and an excellent long-term jitter of less than 3 ns.

J. Appl. Cryst. (2009). 42, 906-916
doi: 10.1107/S0021889809028374
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An interlaboratory study on artificial and commercial Portland clinker and cements has allowed the reproducibility and uncertainty ranges for the components to be established.

J. Appl. Cryst. (2009). 42, 917-924
doi: 10.1107/S0021889809031021
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Fixed-wavelength neutron and multiple-wavelength X-ray powder diffraction are used to assess phase development in alkoxide-derived titania gel as a function of temperature.

J. Appl. Cryst. (2009). 42, 925-931
doi: 10.1107/S0021889809029422
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The degree of agglomeration of epoxy–TiO2 nanocomposites is elucidated by the combined use of X-ray scattering and microscopy.

J. Appl. Cryst. (2009). 42, 932-943
doi: 10.1107/S0021889809032919
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An accurate numerical approach has been implemented for calculating wide-angle X-ray solution scattering patterns of proteins using the traditional scattering model that treats water as a continuum. The results suggest that, at wide angles, the excluded-volume and solvation-layer contributions to scattering cannot be reliably estimated using the continuum representation.

cryocrystallography papers

J. Appl. Cryst. (2009). 42, 944-952
doi: 10.1107/S0021889809023553
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High-quality, ice-free X-ray diffraction data were continuously collected while cryoprotectant-free thaumatin crystals were cooled at 0.1 K s−1 from 300 to 100 K. This establishes the feasibility of fully temperature controlled studies of protein structure and dynamics, and provides insight into how cooling creates crystal disorder.

computer programs

J. Appl. Cryst. (2009). 42, 953-958
doi: 10.1107/S0021889809034062
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An algorithm and the corresponding program SMEPOC have been developed for automatic generation of trial structures for inorganic compounds from the unit-cell content and the space-group information.

J. Appl. Cryst. (2009). 42, 959-964
doi: 10.1107/S0021889809023863
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BioXTAS RAW is a fully open source software program for automated two-dimensional and one-dimensional data reduction and preliminary analysis of isotropic small-angle X-ray scattering data.

J. Appl. Cryst. (2009). 42, 965-974
doi: 10.1107/S0021889809025746
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PolySNAP3 is a computer program for the classification of powder diffraction, spectroscopic and numerical data either separately or combined.

laboratory notes

J. Appl. Cryst. (2009). 42, 975-976
doi: 10.1107/S0021889809028805
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Solidification of the reservoir solution with agarose allows an upside-down sitting-drop plate to be used in a hanging-drop vapor-diffusion crystallization method.

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