Journal of Applied Crystallography

Volume 43, Part 6 (December 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].

• editorial
• research papers
• short communications
• computer programs
• meetings

editorial

J. Appl. Cryst. (2010). 43, 1285-1286  [ doi:10.1107/S0021889810041804 ] Citations in supplementary material M. S. Weiss, H. Einspahr, E. N. Baker, Z. Dauter, A. R. Kaysser-Pyzalla, G. Kostorz and S. Larsen Synopsis: The problem of undercounting of citations that are published only in supplementary material is studied for the journals Nature, Science, Cell and the Proceedings of the National Academy of Sciences (USA). Online 16 November 2010

research papers

J. Appl. Cryst. (2010). 43, 1287-1299  [ doi:10.1107/S0021889810032802 ] Algorithms for the calculation of X-ray diffraction patterns from finite element data E. Wintersberger, D. Kriegner, N. Hrauda, J. Stangl and G. Bauer Synopsis: Efficient algorithms for the simulation of an X-ray diffraction pattern using finite element data as input are developed and applied to concrete problems in semiconductor research. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1300-1304  [ doi:10.1107/S0021889810036472 ] Nanostructural analysis of GaN tripods and hexapods grown on c-plane sapphire S. Lee, Y. Sohn, C. Kim, D. R. Lee and H.-H. Lee Synopsis: Crystallographic and nanostructural analysis of GaN tripods and hexapods was performed using reciprocal-space mapping, transmission electron microscopy and atomistic modelling. Online 13 October 2010

J. Appl. Cryst. (2010). 43, 1305-1313  [ doi:10.1107/S0021889810033868 ] Observation of unusual temperature-dependent stripes in LiTaO3 and LiTaxNb1-xO3 crystals with near-zero birefringence A. M. Glazer, N. Zhang, A. Bartasyte, D. S. Keeble, S. Huband and P. A. Thomas Synopsis: It is found that in LiTaO3 crystals with compositions between congruent and stoichiometric and in mixed LiNbxTa1-xO3 crystals self-organized stripes appear whose widths vary with temperature. They are broad and indistinct when the birefringence is close to zero and become narrower as the temperature is decreased or increased. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1314-1321  [ doi:10.1107/S0021889810038264 ] Field-induced phase transition in Bi1/2Na1/2TiO3-based lead-free piezoelectric ceramics M. Hinterstein, M. Knapp, M. Hölzel, W. Jo, A. Cervellino, H. Ehrenberg and H. Fuess Synopsis: The origin of the electric field-induced strain in the polycrystalline ceramic 0.92Bi1/2Na1/2TiO3-0.06BaTiO3-0.02K1/2Na1/2NbO3 was investigated using in situ high-resolution X-ray and neutron diffraction techniques. Online 13 October 2010

J. Appl. Cryst. (2010). 43, 1322-1328  [ doi:10.1107/S0021889810037210 ] Through-thickness texture profiling by energy dispersive synchrotron diffraction R. S. Coelho, M. Klaus and Ch. Genzel Synopsis: Two different approaches for a through-thickness texture profile assessment applying the energy-dispersive X-ray diffraction method are presented. The conducted measurements should give a first insight into the possibilities of fast and nondestructive texture gradient analyses by means of integrating diffraction methods. Online 13 October 2010

J. Appl. Cryst. (2010). 43, 1329-1337  [ doi:10.1107/S0021889810037222 ] In-crystal chemical ligation for lead compound generation J. Yamane, N. Ohyabu, M. Yao, H. Takemoto and I. Tanaka Synopsis: A new fragment-based growth strategy (in-crystal chemical ligation) for lead compound generation is proposed, which is based on in situ chemical ligation and is operable in X-ray-based fragment screening format. Proof-of-concept experiments demonstrate that protein crystals charged with an anchor molecule not only function as a reaction field for chemical ligation but also serve as a platform on which to select self-assembled products. Online 20 October 2010

J. Appl. Cryst. (2010). 43, 1338-1355  [ doi:10.1107/S002188981003027X ] Inferential statistics of electron backscatter diffraction data from within individual crystalline grains F. Bachmann, R. Hielscher, P. E. Jupp, W. Pantleon, H. Schaeben and E. Wegert Synopsis: Highly concentrated distributed crystallographic orientation measurements within individual crystalline grains are analysed by means of ordinary statistics neglecting their spatial reference. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1356-1371  [ doi:10.1107/S0021889810033418 ] Estimation of errors in diffraction data measured by CCD area detectors D. Waterman and G. Evans Synopsis: A simulation of a CCD area detector is presented. The methods for error estimation on data obtained from images from such detectors by two-dimensional integration are considered and improvements incorporating a realistic instrumental response are suggested. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1372-1376  [ doi:10.1107/S0021889810033649 ] Interesting growth features in potassium dihydrogen phosphate: unravelling the origin and dynamics of point defects in single crystals G. Bhagavannarayana, P. Rajesh and P. Ramasamy Synopsis: Certain interesting growth features of point defects, which commonly occur in single crystals but are difficult to observe directly, such as their origin, clustering and dynamics, have been demonstrated in a potassium dihydrogen phosphate crystal grown at an intentionally fast growth rate by the temperature-lowering method. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1377-1384  [ doi:10.1107/S0021889810034369 ] Asymptotic analysis of small-angle scattering intensities of plane columnar layers S. Ciccariello Synopsis: This paper reports the conditions that make possible the generalization of the Porod law to small-angle scattering intensities collected under grazing incidence. Online 13 October 2010

J. Appl. Cryst. (2010). 43, 1385-1392  [ doi:10.1107/S0021889810035090 ] Scanning small-angle X-ray scattering analysis of the size and organization of the mineral nanoparticles in fluorotic bone using a stack of cards model A. Gourrier, C. Li, S. Siegel, O. Paris, P. Roschger, K. Klaushofer and P. Fratzl Synopsis: A novel procedure is presented for the small-angle X-ray scattering analysis of the organization and size of mineral nanoparticles in pathological bone using a stack of cards model. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1393-1399  [ doi:10.1107/S0021889810033832 ] Determination of twinning relationships between diopside dendrites S.-R. Zhao, H.-J. Xu, H.-W. Liu, R. Mason and H.-F. Liu Synopsis: Novel twining relationships between three diopside dendrite crystals have been found by electron backscattered diffraction. The twin laws and the lattice coincidence have been analysed. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1400-1408  [ doi:10.1107/S0021889810041907 ] Combined in situ small- and wide-angle X-ray scattering studies of TiO2 nanoparticle annealing to 1023 K J. Kehres, J. W. Andreasen, F. C. Krebs, A. M. Molenbroek, I. Chorkendorff and T. Vegge Synopsis: Combined in situ small- and wide-angle X-ray scattering was applied to investigate the dynamical properties of dry oleic acid-capped titanium dioxide nanorods during annealing in an inert gas stream, using a recently developed laboratory setup. Online 9 November 2010

J. Appl. Cryst. (2010). 43, 1409-1414  [ doi:10.1107/S002188981003342X ] Evidence for a non-rhombohedral average structure in the lead-free piezoelectric material Na0.5Bi0.5TiO3 S. Gorfman and P. A. Thomas Synopsis: The average structure of Na0.5Bi0.5TiO3 was found to possess non-rhombohedral symmetry, as supported by the splitting of Bragg peaks in the high-resolution reciprocal space maps. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1415-1418  [ doi:10.1107/S0021889810041282 ] The XIPHOS diffraction facility for extreme sample conditions M. R. Probert, C. M. Robertson, J. A. Coome, J. A. K. Howard, B. C. Michell and A. E. Goeta Synopsis: A new high-intensity laboratory diffractometer has been developed and optimized for single-crystal diffraction experiments under a range of sample environments. Online 29 October 2010

J. Appl. Cryst. (2010). 43, 1419-1425  [ doi:10.1107/S0021889810040951 ] Potential use of ultrasound to promote protein crystallization R. Crespo, P. M. Martins, L. Gales, F. Rocha and A. M. Damas Synopsis: Ultrasound is demonstrated to promote nucleation during protein crystallization by decreasing the energy barrier for crystal formation. Preliminary X-ray diffraction data also support the use of ultrasound to produce higher-quality protein crystals. Online 9 November 2010

J. Appl. Cryst. (2010). 43, 1426-1430  [ doi:10.1107/S0021889810037180 ] A general method to determine twinning elements Y. Zhang, Z. Li, C. Esling, J. Muller, X. Zhao and L. Zuo Synopsis: Based on the minimum shear criterion, a direct and simple method is proposed to calculate twinning elements from the experimentally determined twinning plane for Type I twins or the twinning direction for Type II twins. It is generic and applicable to any crystal structure. Online 9 November 2010

J. Appl. Cryst. (2010). 43, 1431-1439  [ doi:10.1107/S0021889810036782 ] Interface study of a high-performance W/B4C X-ray mirror P. Siffalovic, M. Jergel, L. Chitu, E. Majkova, I. Matko, S. Luby, A. Timmann, S. V. Roth, J. Keckes, G. A. Maier, A. Hembd, F. Hertlein and J. Wiesmann Synopsis: A high-performance W/B4C multilayer mirror was measured by grazing-incidence small-angle X-ray scattering in order to analyse the lateral and vertical correlations of the interface roughness within the framework of a scaling concept of multilayer growth. Thermal stability and oxidation behaviour were also tested. Online 13 October 2010

J. Appl. Cryst. (2010). 43, 1440-1451  [ doi:10.1107/S0021889810037131 ] New approaches to scaling data measured on a CCD diffractometer A. Dudka Synopsis: Effective methods have been developed for empirical data scaling performed after the inclusion of known anisotropic effects that influence the measured intensities of diffraction reflections. Online 20 October 2010

J. Appl. Cryst. (2010). 43, 1456-1463  [ doi:10.1107/S0021889810038148 ] Versatile in situ powder X-ray diffraction cells for solid-gas investigations T. R. Jensen, T. K. Nielsen, Y. Filinchuk, J.-E. Jørgensen, Y. Cerenius, E. M. Gray and C. J. Webb Synopsis: Two multipurpose sample cells of quartz (SiO2) or sapphire (Al2O3) capillaries, developed for the study of solid-gas reactions in dosing or flow mode, are presented. They allow fast change of pressure up to 100 or 300 bar (1 bar = 100 000 Pa) and can also handle solid-liquid-gas studies. Online 20 October 2010

J. Appl. Cryst. (2010). 43, 1464-1473  [ doi:10.1107/S0021889810034114 ] DART: a robust algorithm for fast reconstruction of three-dimensional grain maps K. J. Batenburg, J. Sijbers, H. F. Poulsen and E. Knudsen Synopsis: A novel algorithm is introduced for fast and nondestructive reconstruction of grain maps from X-ray diffraction data. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1474-1478  [ doi:10.1107/S0021889810033856 ] Analysis of the Beaucage model B. Hammouda Synopsis: The Beaucage model has been analyzed carefully. A note of caution is sounded about undesired artefacts produced by this model. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1479-1487  [ doi:10.1107/S002188981003298X ] Instrumental developments for anomalous small-angle X-ray scattering from soft matter systems M. Sztucki, E. Di Cola and T. Narayanan Synopsis: Recent instrumental developments specifically adapted for anomalous small-angle X-ray scattering from charged soft matter are presented. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1488-1494  [ doi:10.1107/S0021889810037969 ] Determination of the -quartz hexagonal cell parameters from a 00.1 neutron multiple diffraction Umweganregung pattern measured at 1003 K L. C. de Campos, C. B. R. Parente and V. L. Mazzocchi Synopsis: This work describes the procedures used to determine the hexagonal cell parameters of -quartz from an experimental 00.1 -quartz neutron multiple diffraction Umweganregung pattern measured at 1003 K. Online 29 October 2010

J. Appl. Cryst. (2010). 43, 1495-1501  [ doi:10.1107/S002188981004149X ] Characterization of the parameters relating adjacent grains using transmission electron microscopy H. W. Jeong, S. M. Seo, H. U. Hong and Y. S. Yoo Synopsis: A method is presented for determining the axis and angle of rotation between two neighbouring grains using a goniometer mounted on a transmission electron microscope. Online 29 October 2010

J. Appl. Cryst. (2010). 43, 1502-1512  [ doi:10.1107/S0021889810041221 ] Substrate-controlled allotropic phases and growth orientation of TiO2 epitaxial thin films V. F. Silva, V. Bouquet, S. Députier, S. Boursicot, S. Ollivier, I. T. Weber, V. L. Silva, I. M. G. Santos, M. Guilloux-Viry and A. Perrin Synopsis: TiO2 thin films were grown by pulsed laser deposition on a wide variety of oxide single-crystal substrates. The effect of the nature and the orientation of the substrate on the phase stabilization and orientation of the films was studied by four-circle X-ray diffraction and the epitaxial relationships were determined. Online 9 November 2010

short communications

J. Appl. Cryst. (2010). 43, 1513-1518  [ doi:10.1107/S0021889810040409 ] Diffraction study of protein crystals grown in cryoloops and micromounts M. A. Berger, J. H. Decker and I. I. Mathews Synopsis: A method for growing crystals on cryoloops or micromounts is described, and diffraction patterns of crystals of three proteins grown by both the new method and the conventional drop method are compared. The study investigates the steps for the automation of the crystal growth and manipulation process and describes the design of a tray for the method. Online 20 October 2010

J. Appl. Cryst. (2010). 43, 1519-1521  [ doi:10.1107/S0021889810038343 ] High diffraction efficiency at hard X-ray energy in a silicon crystal bent by indentation N. Barrière, V. Guidi, V. Bellucci, R. Camattari, T. Buslaps, J. Rousselle, G. Roudil, F.-X. Arnaud, P. Bastie and L. Natalucci Synopsis: The diffraction properties of a crystalline silicon plate of which one face was mechanically indented have been studied. This treatment induced a permanent curvature in the sample, which allowed a diffraction efficiency of 88% for 150 keV photons, i.e. a reflectivity of 64% including the absorption. Online 9 November 2010

computer programs

J. Appl. Cryst. (2010). 43, 1522-1531  [ doi:10.1107/S0021889810032772 ] X+: a comprehensive computationally accelerated structure analysis tool for solution X-ray scattering from supramolecular self-assemblies T. Ben-Nun, A. Ginsburg, P. Székely and U. Raviv Synopsis: This paper describes a user-friendly multi-core accelerated program that fully analyses solution X-ray scattering data. The software is particularly useful for analysing supramolecular self-assemblies and for reconstructing the scattering signal in its entirety. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1532-1534  [ doi:10.1107/S0021889810041543 ] Jpowder: a Java-based program for the display and examination of powder diffraction data A. J. Markvardsen, K. Puphaiboon, M. Arjeneh, K. Shankland, H. L. Guest, T. A. N. Griffin, D. R. Badham and D. W. Flannery Synopsis: The computer program Jpowder, which allows the display and manipulation of powder diffraction data on any internet-capable device that includes a Java Runtime Environment, is described. Online 29 October 2010

J. Appl. Cryst. (2010). 43, 1535-1539  [ doi:10.1107/S0021889810036083 ] Hawk: the image reconstruction package for coherent X-ray diffractive imaging F. R. N. C. Maia, T. Ekeberg, D. van der Spoel and J. Hajdu Synopsis: Hawk is the first publicly available open-source software package for reconstruction of coherent X-ray diffraction images. The large number of implemented algorithms and the ease with which it can be extended make it an ideal framework for the community to test and develop new algorithms. Online 1 October 2010

J. Appl. Cryst. (2010). 43, 1540-1542  [ doi:10.1107/S0021889810038689 ] ResDe: a new tool for visual definition of distance restraints for crystallographic refinement B. J. Hintze and S. J. Johnson Synopsis: ResDe is a suite of programs that allows the user to visually define and edit distance restraints for crystallographic refinement. Online 20 October 2010

J. Appl. Cryst. (2010). 43, 1543-1547  [ doi:10.1107/S0021889810041889 ] DEBUSSY: a Debye user system for nanocrystalline materials A. Cervellino, C. Giannini and A. Guagliardi Synopsis: A suite of programs implementing a fast approach to the Debye function analysis of powder diffraction data from nanocrystalline and/or non-ordered materials is described. Online 9 November 2010

J. Appl. Cryst. (2010). 43, 1548-1552  [ doi:10.1107/S0021889810040963 ] DroplIT, an improved image analysis method for droplet identification in high-throughput crystallization trials P. Vallotton, C. Sun, D. Lovell, V. J. Fazio and J. Newman Synopsis: This article describes a novel automated image analysis methodology affording unprecedented reliability and speed for identifying droplets in large-scale crystallization experiments. Online 29 October 2010

J. Appl. Cryst. (2010). 43, 1553-1559  [ doi:10.1107/S0021889810037209 ] AtomSim: web-deployed atomistic dynamics simulator J. B. Keith, J. R. Fennick, D. R. Nelson, C. E. Junkermeier, J. Y. Y. Lin, C. W. Li, M. M. McKerns, J. P. Lewis and B. Fultz Synopsis: A web-deployed interface has been developed for atomistic simulation with particular emphasis on crystalline materials. Online 9 November 2010

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