Journal of Applied Crystallography

Volume 43, Part 2 (April 2010)

	Cover illustration: PDB_REDO optimization of the oldest structure with experimental data in the PDB [155c; Timkovich & Dickerson (1976). J. Biol. Chem. 251, 4033-4046]. Front: final structure - warmer colours show greater atomic displacement. Back: final structure model with atomic trajectories in yellow. Courtesy of Joosten et al. [J. Appl. Cryst. (2009), 42, 376-384].

• research papers
• cryocrystallography papers
• short communications
• computer programs
• laboratory notes
• meetings

research papers

J. Appl. Cryst. (2010). 43, 227-236  [ doi:10.1107/S0021889809054983 ] Local atomic structure in tetragonal pure ZrO2 nanopowders L. M. Acuña, D. G. Lamas, R. O. Fuentes, I. O. Fábregas, M. C. A. Fantini, A. F. Craievich and R. J. Prado Synopsis: The local atomic order of nanocrystalline pure ZrO2 powders exhibiting the tetragonal phase, synthesized by different wet-chemical routes, has been investigated by extended X-ray absorption fine structure spectroscopy (EXAFS). It was found that the crystallographic model widely accepted for the tetragonal phase does not fit the EXAFS data and, thus, alternative models were explored. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 237-243  [ doi:10.1107/S002188981000138X ] Quality control of protein standards for molecular mass determinations by small-angle X-ray scattering S. Akiyama Synopsis: A simple but effective protocol by which to prepare monodispersed protein standards for molecular mass determinations by small-angle X-ray scattering is described. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 244-249  [ doi:10.1107/S0021889809055113 ] Critical region and metal-nonmetal transition in expanded fluid mercury: advanced evaluation of small-angle X-ray scattering data W. Ruland and F. Hensel Synopsis: The small-angle X-ray scattering data of expanded fluid mercury in the critical region and the metal-nonmetal transition have been interpreted in terms of a two-phase system. The results shed new light on the structure of mercury in this region. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 250-255  [ doi:10.1107/S0021889810002438 ] Accelerated computation of diffuse scattering patterns and application to magnetic neutron scattering M. J. Gutmann Synopsis: The method of computing reciprocal-space planes containing diffuse scattering patterns from a model crystal using lots has been extended to include magnetic scattering. A speed increase of at least an order of magnitude is obtained when performing these computations on currently available graphics processing units. Online 2 March 2010

J. Appl. Cryst. (2010). 43, 256-263  [ doi:10.1107/S0021889810002542 ] Analytical description of the scattering of cellulose nanocrystals in tracheid wood cells M. Ogurreck and M. Müller Synopsis: A model is described which allows the azimuthal X-ray diffraction pattern to be calculated for any hkl reflection of tracheid cells in any orientation. The same description can also be applied to fibers with an additional level of organization, e.g. twisted fibers. Online 5 March 2010

J. Appl. Cryst. (2010). 43, 264-268  [ doi:10.1107/S0021889810005248 ] Focal construct geometry - a novel approach to the acquisition of diffraction data K. Rogers, P. Evans, J. Rogers, J. Chan and A. Dicken Synopsis: A new method of acquiring powder diffraction data by translation rather than rotation of the detector is described. Initial experimental data are presented and further applications of the approach discussed. Online 11 March 2010

J. Appl. Cryst. (2010). 43, 269-275  [ doi:10.1107/S002188981000083X ] A system of metrically invariant relations between the moduli squares of reciprocal-lattice vectors in one-, two- and three-dimensional space D. Stöckelmann, H. Kroll, W. Hoffmann and R. Heinemann Synopsis: A system of one-, two- and three-dimensional metrically independent relations between the squared moduli of reciprocal-lattice vectors (Q values) is developed. The relations generalize and thereby resolve the earlier special Runge-de Wolff approach to indexing unknown powder patterns. Online 11 March 2010

J. Appl. Cryst. (2010). 43, 276-279  [ doi:10.1107/S0021889809055459 ] Twinning structures in near-stoichiometric lithium niobate single crystals S. Yao, X. Hu, T. Yan, H. Liu, J. Wang, X. Qin and Y. Chen Synopsis: The twin structure of a near-stoichiometric lithium niobate single crystal was observed and analyzed by transmission synchrotron topography. The formation mechanism of these twins is discussed. Online 5 March 2010

J. Appl. Cryst. (2010). 43, 280-284  [ doi:10.1107/S0021889810000749 ] Differential quantitative analysis of background structure in energy-filtered convergent-beam electron diffraction patterns P. N. H. Nakashima and B. C. Muddle Synopsis: The background remaining in energy-filtered convergent-beam electron diffraction (CBED) patterns is composed of a slowly varying diffuse component and a signal of much higher angular frequency that mimics the distribution of the elastic signal within each reflection. A model for this background is proposed and verified by a differential analysis of some experimental energy-filtered CBED patterns. This work paves the way for a new approach to quantitative CBED. Online 2 March 2010

J. Appl. Cryst. (2010). 43, 285-292  [ doi:10.1107/S0021889810001846 ] Simulation of modulated reflections J. J. Lovelace, M. D. Winn and G. E. O. Borgstahl Synopsis: Methods for studying simulated modulated protein crystals via supercells were evaluated using existing protein crystallographic software packages. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 293-296  [ doi:10.1107/S0021889810001652 ] Calibration of a silicon crystal for absolute nuclear spectroscopy E. Massa, G. Mana, U. Kuetgens and L. Ferroglio Synopsis: A silicon crystal has been designed for application in both triple Laue interferometry and double Laue diffractometry and its (220) lattice-plane spacing has been calibrated by combined X-ray and optical interferometry to within a 5 × 10-9 relative uncertainty. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 297-307  [ doi:10.1107/S0021889810002050 ] Optimizing high-pressure pair distribution function measurements in diamond anvil cells K. W. Chapman, P. J. Chupas, G. J. Halder, J. A. Hriljac, C. Kurtz, B. K. Greve, C. J. Ruschman and A. P. Wilkinson Synopsis: An effective approach to collecting high-pressure X-ray total scattering data yielding high-resolution pair distribution functions for samples within a diamond anvil cell is presented, which takes into account the parallel optimization of beamline configuration, pressure-cell parameters and data reduction. Online 2 March 2010

J. Appl. Cryst. (2010). 43, 308-319  [ doi:10.1107/S0021889809052339 ] Morphological study of Czochralski-grown lanthanide orthovanadate single crystals and implications on the mechanism of bulk spiral formation H. Cong, H. Zhang, S. Sun, Y. Yu, W. Yu, H. Yu, J. Zhang, J. Wang and R. I. Boughton Synopsis: Large-sized monoclinic LaVO4 crystals have been successfully obtained in the Czochralski method by employing proper seeds to suppress the severe bulk spiral growth. A triggering mechanism has also been proposed to account for the influence of seeds on the bulk spiral formation, a problem that is becoming increasingly urgent in growing low-symmetry oxide crystals. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 320-327  [ doi:10.1107/S0021889809051395 ] Crystal structure of cobalt-substituted calcium hydroxyapatite nanopowders prepared by hydrothermal processing L. Veselinovic, L. Karanovic, Z. Stojanovic, I. Bracko, S. Markovic, N. Ignjatovic and D. Uskokovic Synopsis: A series of cobalt-exchanged hydroxyapatite (CoHAp) powders with different Ca/Co ratios and nominal unit-cell contents Ca10-xCox(PO4)6(OH)2, x = 0, 0.5, 1.0, 1.5 and 2.0, were synthesized by hydrothermal treatment of a precipitate at 473 K for 8 h. The effects of cobalt content on the CoHAp powders were investigated using inductively coupled plasma emission spectroscopy, particle size analysis, transmission electron microscopy and high-resolution transmission electron microscopy analyses, as well as X-ray powder diffraction including Rietveld analysis. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 328-336  [ doi:10.1107/S0021889810005595 ] The crystal structure of perdeuterated methanol hemiammoniate (CD3OD·0.5ND3) determined from neutron powder diffraction data at 4.2 and 180 K A. D. Fortes, I. G. Wood and K. S. Knight Synopsis: The structure of the 2:1 compound in the system methanol-ammonia has been determined from high-resolution neutron powder diffraction; the methyl groups are found to be orientationally ordered at 4.2 K but become disordered at 180 K. Online 2 March 2010

J. Appl. Cryst. (2010). 43, 337-340  [ doi:10.1107/S0021889810004759 ] Photocrystallography - design and methodology for the use of a light-emitting diode device S. K. Brayshaw, J. W. Knight, P. R. Raithby, T. L. Savarese, S. Schiffers, S. J. Teat, J. E. Warren and M. R. Warren Synopsis: The design of a light-emitting diode array device suitable for use in single-crystal X-ray photocrystallographic experiments is presented, together with a description of the experimental methodology employed in these experiments. Online 5 March 2010

cryocrystallography papers

J. Appl. Cryst. (2010). 43, 341-346  [ doi:10.1107/S0021889809054272 ] Semi-automated protein crystal mounting device for the sulfur single-wavelength anomalous diffraction method Y. Kitago, N. Watanabe and I. Tanaka Synopsis: A new semi-automated protein crystal mounting device has been developed for the capillary-top mounting method, which has advantages for the sulfur single-wavelength anomalous diffraction phasing method using longer-wavelength X-rays. Online 12 February 2010

short communications

J. Appl. Cryst. (2010). 43, 347-349  [ doi:10.1107/S0021889810002451 ] Characteristics of the SAS correlation function of long cylinders with oval right section W. Gille Synopsis: The characteristic features of the small-angle scattering (SAS) correlation function of long cylinders with oval right section are described. Online 2 March 2010

J. Appl. Cryst. (2010). 43, 350-351  [ doi:10.1107/S002188981000467X ] Diffraction gratings as small-angle X-ray scattering calibration standards K. Nygård, O. Bunk, E. Perret, C. David and J. F. van der Veen Synopsis: It is demonstrated that diffraction gratings can be used as accurate momentum-transfer calibration standards in small-angle X-ray scattering experiments. Online 5 March 2010

computer programs

J. Appl. Cryst. (2010). 43, 352-355  [ doi:10.1107/S0021889810001937 ] CONEX, a program for angular calibration and averaging of two-dimensional powder scattering patterns C. J. Gommes and B. Goderis Synopsis: CONEX is a Windows application for converting X-ray powder patterns measured on flat two-dimensional detectors into one-dimensional scattering patterns. It is based on the rigorous use of calibration samples to determine the three-dimensional position of the detector, which enables one to correct the data for geometrical distortions, even when the detector is highly tilted and not centered on the beam. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 356-361  [ doi:10.1107/S0021889809054326 ] Efficient molecular surface rendering by linear-time pseudo-Gaussian approximation to Lee-Richards surfaces (PGALRS) H. J. Bernstein and P. A. Craig Synopsis: By contouring the density resulting from the summation of pseudo-Gaussian atoms an approximation to the Lee-Richards surface of a molecule can be computed in linear time, allowing rapid identification of surface atoms and residues. This allows accurate calculation of molecular surface areas and rendering of approximate molecular surfaces to be extended to larger macromolecules than is currently feasible. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 362-366  [ doi:10.1107/S0021889810000452 ] WebCSD: the online portal to the Cambridge Structural Database I. R. Thomas, I. J. Bruno, J. C. Cole, C. F. Macrae, E. Pidcock and P. A. Wood Synopsis: The new web-based application WebCSD is introduced, which provides a range of facilities for searching the Cambridge Structural Database within a standard web browser. Search options within WebCSD include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 367-369  [ doi:10.1107/S002188981000110X ] AMINONET - a tool to construct and visualize amino acid networks, and to calculate topological parameters Md. Aftabuddin and S. Kundu Synopsis: AMINONET is a Java-based software tool to construct and visualize different protein contact networks (unweighted and weighted; long range, short range and any range; hydrophobic, hydrophilic, charged or all-amino-acid networks). The software will also help in calculating the values of the different topological parameters of the constructed networks to understand the structure-function relationship. Online 12 February 2010

J. Appl. Cryst. (2010). 43, 370-376  [ doi:10.1107/S0021889810005509 ] PSSP, a computer program for the crystal structure solution of molecular materials from X-ray powder diffraction data S. Pagola and P. W. Stephens Synopsis: This article describes the computer program PSSP (powder structure solution program) and the related simulated annealing-based methodology used for the crystal structure determination of molecular solids from X-ray powder diffraction data. Online 11 March 2010

laboratory notes

J. Appl. Cryst. (2010). 43, 377-379  [ doi:10.1107/S0021889810003614 ] A 100-position robotic sample changer for powder diffraction with low-background vacuum chamber S. R. Olsen, S. A. Pullen and M. Avdeev Synopsis: A robotic sample changer has been designed and built to be used for neutron powder diffraction experiments at the Australian OPAL research reactor. Online 11 March 2010

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