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Journal logoJOURNAL OF
ISSN: 1600-5767

February 2008 issue

Highlighted illustration

Cover illustration: Two-dimensional grazing-incidence X-ray scattering pattern for a PS-b-PI thin film deposited on a silicon substrate. Courtesy of Sangwoo Jin et al. [J. Appl. Cryst. (2007), 40, 950-958].

research papers

J. Appl. Cryst. (2008). 41, 1-7
doi: 10.1107/S0021889807048820
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High-density amorphous ice is shown to occur in high-pressure cryocooled protein crystallization solution and protein crystals, supporting a proposed mechanism for high-pressure cryocooling effects.

J. Appl. Cryst. (2008). 41, 8-17
doi: 10.1107/S0021889807049308
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The statistical distribution of wavelet coefficient values in each sub-band image is used to provide variables for the classification of images from protein crystallization experiments.

J. Appl. Cryst. (2008). 41, 18-26
doi: 10.1107/S0021889807049886
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A method is developed for an exact calculation of the intensity of X-ray diffraction along a crystal truncation rod.

J. Appl. Cryst. (2008). 41, 27-30
doi: 10.1107/S0021889807049655
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Through an X-ray scattering analysis, the short-range structural features, the relationship(s) between the aryl/alkyl carbon ratio, and the size of the average polycyclic aromatic unit in Ledo coal from Makum coalfield, Assam, India, are elucidated.

J. Appl. Cryst. (2008). 41, 31-37
doi: 10.1107/S0021889807049898
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A new way for evaluating the quality of crystallographic electron density maps is described. It has been found that a high-quality map possesses greater robustness against perturbations applied to the phases.

J. Appl. Cryst. (2008). 41, 38-43
doi: 10.1107/S0021889807050029
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Improved post-perovskite structure models of MgGeO3 (Cmcm) are obtained via development of a new graphite gasket for the diamond anvil cell which increases the volume of sample and quality of diffraction data at pressures near 100 GPa. These models agree with a structure survey supporting a new method for estimating the Clapeyron slope between perovskite (Pbnm) and post-perovskite structures of MgSiO3.

J. Appl. Cryst. (2008). 41, 44-55
doi: 10.1107/S0021889807051175
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A consistent scheme for describing the geometry of X-ray stress acquisition is proposed. It allows derivation of all the classical acquisition modes described in the literature by distinguishing angles related to the physics of diffraction, angles related to the goniometer and angles probing the specimen.

J. Appl. Cryst. (2008). 41, 56-61
doi: 10.1107/S0021889807054192
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The procedure implemented in a previous version of EXPO combining a Monte Carlo approach with the information contained in the Fourier map as obtained at the end of a direct-methods procedure has been revised and improved.

J. Appl. Cryst. (2008). 41, 62-67
doi: 10.1107/S0021889807054398
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The phased rotation, conformation and translation function was applied to nucleic acid structures; the search fragment is a mononucleotide extended by a phosphate group. 50 to 93% of fragments can be located depending on the resolution and phase quality.

J. Appl. Cryst. (2008). 41, 68-82
doi: 10.1107/S0021889807054453
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Models of (MgCl2)x polynuclear structures are built and a method for the calculation of the X-ray powder diffraction patterns of the models is devised. The calculated diffraction patterns of these model structures may be useful to interpret the structural evolution of solid solvates of MgCl2 with Lewis bases during the preparation of the heterogeneous catalyst systems used for Ziegler–Natta polymerization of olefins.

J. Appl. Cryst. (2008). 41, 83-95
doi: 10.1107/S002188980705621X
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New methods for determination of the site occupancy factors in noncentrosymmetric crystals using reductions of the anomalous scattering contribution and the intermeasurement minimization method are described

J. Appl. Cryst. (2008). 41, 96-103
doi: 10.1107/S0021889807059870
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A description is given of a maximum-likelihood approach to absolute structure determinations of biologically active molecules.

J. Appl. Cryst. (2008). 41, 104-109
doi: 10.1107/S0021889807065235
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Uptake of metal ions by proteins can be predicted on the basis of the amino acid composition, by using a mixture of several simplified amino acid alphabets and by employing machine learning methods, with 70–90% accuracy, depending on the type of metal.

J. Appl. Cryst. (2008). 41, 110-114
doi: 10.1107/S0021889807048765
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The correct three-dimensional shape of the accessible reciprocal-space region for a given plane of incidence is plotted and formulae for finding the experimental geometry for any reciprocal node are given.

J. Appl. Cryst. (2008). 41, 115-123
doi: 10.1107/S002188980704976X
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Simple equations of the diffraction and reflection conics as second degree polynomials in the receiving-slit plane of a Bragg–Brentano diffractometer are given and applied to the analysis of the instrument functions.

J. Appl. Cryst. (2008). 41, 124-133
doi: 10.1107/S0021889807050005
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The performance of a diffractometer equipped with a rotating anode source, a single-reflection collimating multilayer optic which can collimate an X-ray beam in two mutually perpendicular planes and a parallel-plate collimator in front of the detector has been characterized in detail. Its capabilities have been illustrated by ray-tracing calculations for the multilayer optic and by standard powder diffraction experiments.

J. Appl. Cryst. (2008). 41, 134-142
doi: 10.1107/S0021889807051345
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The multiple scattering effects present in grazing-incidence small-angle X-ray scattering (GISAXS) data and interference between them are addressed theoretically as well as experimentally with measurement of a series of patterns at different incident angles, referred to as `incident-angle-resolved GISAXS' (IAR-GISAXS). X-ray reflectivity, GISAXS and IAR-GISAXS of virus particles on Si-substrate supported-polystyrene films have been measured and all the data have been analyzed with appropriate formalisms.

J. Appl. Cryst. (2008). 41, 143-152
doi: 10.1107/S0021889807051904
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Results of the first world-wide round-robin experiment on X-ray reflectometry (XRR) are presented and discussed. The investigation aims to assess the reproducibility of XRR measurements and analysis, and to produce a `good practice' manual for this technique.

J. Appl. Cryst. (2008). 41, 153-160
doi: 10.1107/S0021889807055069
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An X-ray tracing program was developed to simulate the instrument function of a laboratory high-resolution X-ray powder diffractometer. The results provide the basis for discussing the opportunity of using X-ray tracing in diagram-refinement software.

J. Appl. Cryst. (2008). 41, 161-166
doi: 10.1107/S0021889807056361
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High-resolution neutron scattering data down to q = 4 × 10−3 nm−1 can be obtained using the very small angle neutron scattering spectrometer under construction at the Laboratoire Léon Brillouin. While still under construction, the new instrument has successfully allowed completion of the scattering curve of vesicles of 500 nm radii toward the smaller scattering vector range.

J. Appl. Cryst. (2008). 41, 167-175
doi: 10.1107/S0021889807056944
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A user-friendly high-pressure cell for synchrotron small-angle X-ray scattering studies of protein solutions is described. Disposable inner sample cells facilitate sample isolation, minimization and handling.

J. Appl. Cryst. (2008). 41, 176-184
doi: 10.1107/S0021889807057822
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Web-Ice is a scalable, extendable and portable software application for rapid on-line diffraction image analysis, autoindexing and strategy calculation. The Web-Ice architecture, software components and functionality, both as a stand-alone application and as part of a beamline control system, are described.

J. Appl. Cryst. (2008). 41, 185-190
doi: 10.1107/S0021889807058074
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A novel method for focusing X-rays in two dimensions by thermal-gradient crystals in symmetrical Laue geometry is described. The intensity in the focal point can be increased significantly by using thermal-gradient crystals.

J. Appl. Cryst. (2008). 41, 191-197
doi: 10.1107/S0021889807064011
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A new method for simply identifying the X-ray diffraction peak broadening caused by tilt and twist distributions through analysis of their hkl dependence is proposed. The method for twist distributions is experimentally demonstrated using GaN epitaxial films on sapphire substrates.

J. Appl. Cryst. (2008). 41, 198-205
doi: 10.1107/S0021889807065806
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A flat-plate single-crystal sample holder is used to place a thin layer of highly absorbing samarium and gadolinium compounds in a neutron beam and obtain Rietveld refinement quality diffraction data in a modest time. Demonstration data are presented on two intermetallic compounds, Sm3Ag4Sn4 and Gd3Ag4Sn4, and it is shown that both structural and magnetic information can be derived from the diffraction patterns.

short communications

J. Appl. Cryst. (2008). 41, 206-209
doi: 10.1107/S0021889807060803
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Compact, inexpensive, easily constructed sample holders for fiber diffraction allow humidity control, stretching and exposure to magnetic fields during fiber preparation, and primary containment for toxic and infectious biological materials.

J. Appl. Cryst. (2008). 41, 210-213
doi: 10.1107/S0021889807055458
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The paper discusses the role of stress on displacive phase transformations where plasticity is associated with variant selection, together with its implications for the resulting texture.

J. Appl. Cryst. (2008). 41, 214-216
doi: 10.1107/S0021889807057251
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A small, simple and inexpensive capillary furnace has been developed for variable-temperature X-ray diffraction of liquid crystals and other organic materials.

computer programs

J. Appl. Cryst. (2008). 41, 217-218
doi: 10.1107/S0021889807050054
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Two programs are presented that facilitate the transition to refining macromolecular data with the SHELX suite. mtz2sca is used to convert data processed and integrated with MOSFLM into sca format for further processing with SHELXC and SHELXD; mtz2hkl is used to convert an mtz file used for refinement in REFMAC5 into \tt HKLF 3 or \tt 4 format for refinement with SHELXL or SHELXH.

J. Appl. Cryst. (2008). 41, 219-221
doi: 10.1107/S0021889807053708
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The web-based interactive computing server RPMS was developed to visualize the conformational angles (φ and ψ) of multiple highly homologous protein structures in a single Ramachandran plot.

J. Appl. Cryst. (2008). 41, 222-226
doi: 10.1107/S0021889807055136
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A description is given of software that allows small-angle neutron contrast variation data of two-component biomolecular assemblies to be analysed in a straightforward manner.

international union of crystallography

J. Appl. Cryst. (2008). 41, 227-232
doi: 10.1107/S0021889807060037

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