[IUCr 2014 Congress]

[International School of Crystallization (ISC) 2014]

Journal of Applied Crystallography

Volume 47, Part 2 (April 2014)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: A TEM image of a representative region of a CdS nanoparticle sample, overlaid with depictions of the spheroidal morphology and atomic structure of CdS nanoparticles obtained from (top) a pair distribution function (PDF) fit and (bottom) a PDF/small-angle X-ray scattering co-refinement. Courtesy of Farrow et al. [J. Appl. Cryst. (2014), 47, 561-565.

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J. Appl. Cryst. (2014). 47, 488-494  [ doi:10.1107/S1600576714000314 ]

Energy-dispersive X-ray diffraction mapping on a benchtop X-ray fluorescence system

D. W. Lane, A. Nyombi and J. Shackel

Synopsis: A method for energy-dispersive X-ray diffraction mapping is presented, using a conventional low-power benchtop X-ray fluorescence spectrometer. Maps are presented for Bi, Pb and steel shot gun pellets and the capability for lower atomic number and lower-symmetry materials is briefly explored.

Online 22 February 2014


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J. Appl. Cryst. (2014). 47, 495-504  [ doi:10.1107/S1600576714000557 ]

Sub-micrometre depth-gradient measurements of phase, strain and texture in polycrystalline thin films: a nano-pencil beam diffraction approach

N. Vaxelaire, P. Gergaud and G. B. M. Vaughan

Synopsis: A single-scan approach to evaluating chemical and structural gradients in polycrystalline thin films with a resolution of tens of nanometres is reported. Thinned samples are measured in cross section in transmission geometry with a high-energy X-ray nano-pencil beam.

Online 22 February 2014


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J. Appl. Cryst. (2014). 47, 505-510  [ doi:10.1107/S1600576713034316 ]

Mini droplets to super droplets: evolution of self-assembled Au droplets on GaAs(111)B and (110)

M. Sui, M.-Y. Li, E.-S. Kim and J. Lee

Synopsis: Under identical growth conditions, self-assembled Au droplets show significantly different size and density depending on the amount of Au deposition. With relatively low Au deposition amounts, below 3 nm, round dome-shaped mini Au droplets with high packing density can be fabricated, while super large Au droplets result with higher deposition amounts, above 10 nm, with a density two orders of magnitude lower.

Online 22 February 2014


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J. Appl. Cryst. (2014). 47, 511-526  [ doi:10.1107/S1600576713034158 ]

Rietveld-based energy-dispersive residual stress evaluation: analysis of complex stress fields [sigma]ij(z)

D. Apel, M. Klaus, M. Genzel and C. Genzel

Synopsis: Energy-dispersive synchrotron diffraction was applied to analyse the near-surface residual stress state in polycrystalline materials. A Rietveld-based formalism is introduced which permits a full triaxial data evaluation and, therefore, even the detection of out-of-plane [sigma]33(z) gradients.

Online 22 February 2014


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J. Appl. Cryst. (2014). 47, 527-531  [ doi:10.1107/S1600576713034535 ]

Synthesis, formation mechanism and photoelectric properties of GeS nanosheets and nanowires

L. Shi and Y. Dai

Synopsis: Single-crystalline GeS nanosheets and nanowires can be selectively synthesized by changing the reaction conditions. The samples were characterized using X-ray powder diffraction, transmission electron microscopy, energy-dispersive X-ray spectrometry and scanning electron microscopy. The growth mechanism of GeS nanowires is proposed to be via a rolling-up process.

Online 22 February 2014


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J. Appl. Cryst. (2014). 47, 532-538  [ doi:10.1107/S1600576713034560 ]

A symmetry-mode description of rigid-body rotations in crystalline solids: a case study of Mg(H2O)6RbBr3

M. Müller, R. E. Dinnebier, A.-C. Dippel, H. T. Stokes and B. J. Campbell

Synopsis: The parametric refinement of rotational rigid-body symmetry modes is demonstrated for the cubic monoclinic phase transition in Mg(H2O)6RbBr3.

Online 22 February 2014


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J. Appl. Cryst. (2014). 47, 539-543  [ doi:10.1107/S1600576713033943 ]

Computer models of icosahedral carbon nanostructures (shungite)

V. Pleshakov

Synopsis: A universal algorithm for the generation of three-dimensional models of icosahedral fullerene-like carbon nanostructures has been developed.

Online 22 February 2014


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J. Appl. Cryst. (2014). 47, 544-551  [ doi:10.1107/S1600576713034547 ]

Approaches to modelling thermal diffuse scattering in triglycine sulfate, (NH2CH2COOH)3·H2SO4

J. M. Hudspeth, D. J. Goossens and T. R. Welberry

Synopsis: The displacive diffuse scattering from triglycine sulfate, (NH2CH2COOH)3·H2SO4, has been modelled using several approaches, to determine which is preferable and as a guide for analysis of similar compounds.

Online 22 February 2014


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J. Appl. Cryst. (2014). 47, 552-560  [ doi:10.1107/S1600576714000375 ]

Modelling and quantification of intergrowth in [gamma]-MnO2 by laboratory pair distribution function analysis

K. Galliez, P. Deniard, P.-E. Petit, D. Lambertin, F. Bart and S. Jobic

Synopsis: The application of the atomic pair distribution function for the purpose of obtaining the intergrowth amount of pyrolusite ([beta]-MnO2) and ramsdellite (R-MnO2) in [gamma]-MnO2 is demonstrated. The presented model opens the door to intergrowth quantification in numerous materials where the two structural components are clearly distinguishable.

Online 22 February 2014


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J. Appl. Cryst. (2014). 47, 561-565  [ doi:10.1107/S1600576713034055 ]

Robust structure and morphology parameters for CdS nanoparticles by combining small-angle X-ray scattering and atomic pair distribution function data in a complex modeling framework

C. Farrow, C. Shi, P. Juhás, X. Peng and S. J. L. Billinge

Synopsis: A complex modeling approach that combines atomic pair distribution function and small-angle X-ray scattering data from CdS quantum dots yields more robust and accurate structural and morphological parameters when compared with either single technique alone.

Online 11 March 2014


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J. Appl. Cryst. (2014). 47, 566-574  [ doi:10.1107/S1600576714000454 ]

Temperature-dependent optical rotatory power in the presence of birefringence of KTA and KTP crystals by the high-accuracy universal polarimeter method at 632.8 nm wavelength

C. Hernández-Rodríguez, A. B. Fragoso-López, J. Herreros-Cedrés and R. Guerrero-Lemus

Synopsis: Temperature-dependent optical rotatory power can give valuable information on the achiral optical properties of orthorhombic crystals of which only a few measurements are known. The high-accuracy universal polarimeter technique was successfully applied to determine the optical rotation in the presence of birefringence of potassium titanyl arsenate (KTA) and potassium titanyl phosphate (KTP) biaxial crystals.

Online 11 March 2014


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J. Appl. Cryst. (2014). 47, 575-583  [ doi:10.1107/S1600576714000569 ]

A method for accurate texture determination of thin oxide films by glancing-angle laboratory X-ray diffraction

A. Garner, M. Preuss and P. Frankel

Synopsis: A method for accurate measurement of the texture of thin oxide films has been proposed. The method involves the separation of integrated intensities from complex glancing-angle diffraction spectra and leads to an improved representation of the preferred orientation present in oxide films.

Online 11 March 2014


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J. Appl. Cryst. (2014). 47, 584-592  [ doi:10.1107/S1600576714000855 ]

Towards a high-throughput system for high-pressure cooling of cryoprotectant-free biological crystals

P. van der Linden, F. Dobias, H. Vitoux, U. Kapp, J. Jacobs, S. Mc Sweeney, C. Mueller-Dieckmann and P. Carpentier

Synopsis: A high-pressure system for cooling cryoprotectant-free biological crystals has been designed for automated data collection on synchrotrons. The apparatus and the method have been validated with a series of test samples.

Online 11 March 2014


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J. Appl. Cryst. (2014). 47, 593-598  [ doi:10.1107/S1600576714000922 ]

Robust powder auto-indexing using many peaks

R. Oishi-Tomiyasu

Synopsis: A new algorithm, CONOGRAPH, carries out exhaustive powder auto-indexing in a short time, even if the q values of many peaks are used for robust powder auto-indexing. Some results from CONOGRAPH are presented.

Online 11 March 2014


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J. Appl. Cryst. (2014). 47, 599-605  [ doi:10.1107/S1600576714001964 ]

Neutron diffraction studies of a double-crystal (+n,-m) setting containing a fully asymmetric diffraction geometry of a bent perfect crystal with output beam expansion

P. Mikula, M. Vrána, J. Pilch, B. Seok Seong, W. Woo and V. Em

Synopsis: This article desribes the neutron diffraction properties of a double-crystal (+n,-m) setting, which contains a bent perfect Si(311) crystal in the fully asymmetric diffraction (FAD) geometry with output beam expansion and a bent perfect Si(220) crystal in the symmetric diffraction geometry. After beam expansion, this FAD geometry provides a beam of large cross section but small divergence.

Online 11 March 2014


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J. Appl. Cryst. (2014). 47, 606-612  [ doi:10.1107/S1600576714001939 ]

Crystallographic effect of a high magnetic field on a solidified hypoeutectic Zn-Al alloy

L. Li, Z. Li, Y. Zhang, C. Esling, H. Liu, Z. Zhao, Q. Zhu, Y. Zuo and J. Cui

Synopsis: Crystallographic features of a hypoeutectic Zn-Al alloy were significantly affected by the presence of a high magnetic field during the solidification process.

Online 11 March 2014


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J. Appl. Cryst. (2014). 47, 613-618  [ doi:10.1107/S160057671400168X ]

On the assessment by grazing-incidence small-angle X-ray scattering of replica quality in polymer gratings fabricated by nanoimprint lithography

M. Soccio, N. Alayo, I. Martín-Fabiani, D. R. Rueda, M. C. García-Gutiérrez, E. Rebollar, D. E. Martínez-Tong, F. Pérez-Murano and T. A. Ezquerra

Synopsis: It is shown using grazing-incidence small-angle X-ray scattering experiments that a series of NIL polymer gratings with different line quality present characteristic features that can be associated with the level of defects per line.

Online 19 March 2014


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J. Appl. Cryst. (2014). 47, 619-629  [ doi:10.1107/S1600576714001046 ]

Combined fitting of small- and wide-angle X-ray total scattering data from nanoparticles: benefits and issues

A. Gagin, A. J. Allen and I. Levin

Synopsis: Simultaneous fitting of small- and wide-angle neutron/X-ray total scattering data for nanoparticles has been evaluated using both simulated and experimental signals.

Online 19 March 2014


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J. Appl. Cryst. (2014). 47, 630-641  [ doi:10.1107/S1600576714001691 ]

Moroccan ornamental quasiperiodic patterns constructed by the multigrid method

Y. Aboufadil, A. Thalal and M. A. E. I. Raghni

Synopsis: Quasiperiodic tilings constructed by the multigrid method and decorated by rosettes constructed by craftsmen are studied.

Online 19 March 2014


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J. Appl. Cryst. (2014). 47, 642-653  [ doi:10.1107/S1600576714001216 ]

Small-angle scattering from polydisperse particles with a diffusive surface

O. V. Tomchuk, L. A. Bulavin, V. L. Aksenov, V. M. Garamus, O. I. Ivankov, A. Y. Vul', A. T. Dideikin and M. V. Avdeev

Synopsis: Small-angle scattering from polydisperse non-homogeneous particles with a diffusive interface is considered for the case of low diffusivity. The deduced simplifications in the analysis of both the polydispersity and the inner structure (contrast variation) of the particles are used in the treatment of small-angle neutron scattering data from liquid dispersions of detonation nanodiamond.

Online 19 March 2014


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J. Appl. Cryst. (2014). 47, 654-658  [ doi:10.1107/S1600576714002210 ]

Absolute scale calibration with use of excess scattering length for small-angle X-ray scattering

N. Ohta, H. Sekiguchi, Y. C. Sasaki and N. Yagi

Synopsis: 1-Chlorododecane dispersed in dodecane is proposed as an absolute scale calibration standard substance for small-angle X-ray scattering.

Online 19 March 2014


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[HTML version][PDF version][CIF][3d view][Structure Factors][Supplementary Material]  [Buy article online]

J. Appl. Cryst. (2014). 47, 659-667  [ doi:10.1107/S1600576714003379 ]

Simultaneous determination of several crystal structures from powder mixtures: the combination of powder X-ray diffraction, band-target entropy minimization and Rietveld methods

M. Schreyer, L. Guo, S. Thirunahari, F. Gao and M. Garland

Synopsis: By collecting multiple mixture powder diffractograms and deconvoluting them into the individual components using the band target entropy minimization algorithm, single-phase powder diffractograms are obtained. From these, structure solutions and refinements are achieved with standard crystallographic techniques.

Online 19 March 2014


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J. Appl. Cryst. (2014). 47, 668-679  [ doi:10.1107/S1600576714003240 ]

LCDiXRay: a user-friendly program for powder diffraction indexing of columnar liquid crystals

N. Godbert, A. Crispini, M. Ghedini, M. Carini, F. Chiaravalloti and A. Ferrise

Synopsis: LCDiXRay, a user-friendly program for the indexing of powder X-ray diffraction patterns of columnar liquid crystals, is presented. The program allows straightforward determination of structural parameters of columnar mesophases.

Online 19 March 2014


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J. Appl. Cryst. (2014). 47, 680-683  [ doi:10.1107/S1600576714004464 ]

Patterson analysis for layer profile determination by neutron or X-ray reflectometry. II

Z. Tun

Synopsis: A way of determining layer structure in terms of Patterson analysis is demonstrated for a simulated X-ray reflectometry measurement. This article is the sequel to a recent publication where the technique was demonstrated for neutron reflectometry.

Online 19 March 2014


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J. Appl. Cryst. (2014). 47, 684-691  [ doi:10.1107/S1600576714003331 ]

Metastable adaptive orthorhombic martensite in zirconia nanoparticles

S. Liu, W. Hu, Y. Zhang, J. Xiang, F. Wen, B. Xu, J. He, D. Yu, Y. Tian and Z. Liu

Synopsis: Owing to the constraint of the twinning interface in tetragonal zirconia nanoparticles, the martensitic transformation induces an adaptive Pbca orthorhombic phase before finally transforming to the monoclinic phase.

Online 19 March 2014


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J. Appl. Cryst. (2014). 47, 692-700  [ doi:10.1107/S1600576714004403 ]

Protein crystal harvesting using the RodBot: a wireless mobile microrobot

H.-W. Tung, D. F. Sargent and B. J. Nelson

Synopsis: A new wireless microdevice manipulates protein crystals using gentle fluid flow. The microrobot is capable of selecting a single crystal from a group and transporting it onto a loop.

Online 19 March 2014


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J. Appl. Cryst. (2014). 47, 701-711  [ doi:10.1107/S1600576714002192 ]

Parameterization of the coupling between strain and order parameter for LuF[SeO3]

O. V. Magdysyuk, M. Müller, R. E. Dinnebier, C. Lipp and T. Schleid

Synopsis: The high-temperature phase transition of LuF[SeO3] has been characterized by time-resolved high-resolution synchrotron powder diffraction, and the coupling between the strain and the displacive order parameter has been analysed by parametric refinement using different models.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 712-718  [ doi:10.1107/S1600576714003835 ]

An iterative method to extract the size distribution of non-interacting polydisperse spherical particles from small-angle scattering data

D. Sen, A. Das and S. Mazumder

Synopsis: A new iterative method can extract the size distribution of non-interacting polydisperse spherical particles from a small-angle scattering profile. This method does not demand the consideration of any basis function or depend on any numerical transform.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 719-725  [ doi:10.1107/S1600576714004658 ]

Therapy modifies cystine kidney stones at the macroscopic scale. Do such alterations exist at the mesoscopic and nanometre scale?

D. Bazin, M. Daudon, G. André, R. Weil, E. Véron and G. Matzen

Synopsis: With an incidence of 1:7000 births, cystinuria is the most frequent genetic disease inducing nephrolithiasis. It is shown that alkalinization with sodium bicarbonate affects cystine kidney stones at the mesoscopic and nanoscopic scales, while other medical treatments only alter their surface, a result which may help to assess the interaction between drugs and cystine stones in cystinuric patients.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 726-731  [ doi:10.1107/S160057671400435X ]

On identification of symmetric and improperly quasi-symmetric grain boundaries

K. Glowinski

Synopsis: New parameters approximating the accurate distances to the nearest symmetric and improperly quasi-symmetric boundaries are defined to speed up analyses of grain boundary networks. The new parameters are used for studies of symmetric and improperly quasi-symmetric boundaries in three-dimensional data of a nickel-based superalloy.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 732-738  [ doi:10.1107/S1600576714002854 ]

Characterization of phase-transition-induced micro-domain structures in vanadium dioxide

P. Lu, J. Zhou, X. Liu, Z. Zhang, F. Xu, L. Zhang, X. Mou, J. Feng, Y. Gao and J. Zhao

Synopsis: All the possible kinds of phase-transition-induced domain structures in the insulating M1 and M2 phases of vanadium dioxide were theoretically predicted using a general space group method and characterized by transmission electron microscopy.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 739-744  [ doi:10.1107/S160057671400377X ]

High-temperature Raman spectroscopy of microstructure around the growing [beta]-BaB2O4 crystal in the BaO-B2O3-Na2O system

S. Liu, G. Zhang, S. Wan, X. Jiang, Y. Wang, Z. Lin and Y. Wu

Synopsis: High-temperature Raman spectroscopy was applied to study the microstructure of the BaO-B2O3-Na2O solution for [beta]-BaB2O4 crystal growth. The Raman spectrum of the growth solution was calculated, and the calculated result coincided well with the experimental result.

Online 28 March 2014


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[HTML version][PDF version][CIF][3d view][Powder data files][Supplementary Material]  [Buy article online]

J. Appl. Cryst. (2014). 47, 745-754  [ doi:10.1107/S1600576714004907 ]

Structure evolution with Sr content of the perovskite-like materials La2-xSrxCoTiO6 (0 [less-than or equal to] x [less-than or equal to] 0.5)

A. Gómez-Pérez, J. C. Pérez-Flores, C. Ritter, K. Boulahya, G. R. Castro, F. García-Alvarado and U. Amador

Synopsis: Substitution in the perovskite A site releases internal structural stress as a result of a better matching of the A-O and B-O distances, leading to less distorted phases (transition from monoclinic to orthorhombic). Symmetry-adapted mode decomposition revealed that the out-of-phase tilt of BO6 octahedra slightly varies with Sr content, whereas the in-phase tilt strongly decreases to almost vanish for x > 0.5, anticipating a transition to a more symmetric structure.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 755-761  [ doi:10.1107/S1600576714004671 ]

Hierarchical O(N) computation of small-angle scattering profiles and their associated derivatives

K. Berlin, N. A. Gumerov, D. Fushman and R. Duraiswami

Synopsis: Structure refinement protocols based on small-angle X-ray scattering iteratively adjust the posited positions of atoms in a structure via a gradient-based constrained optimization to ensure that experimental scattering profile data are matched. This requires computation of the profile and its gradient with respect to atomic coordinates at every step. The fast algorithms proposed in this article reduce these to a cost that is linear in the number of atoms for any specified accuracy.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 762-769  [ doi:10.1107/S1600576714004506 ]

Imaging of strain and lattice orientation by quick scanning X-ray microscopy combined with three-dimensional reciprocal space mapping

G. A. Chahine, M.-I. Richard, R. A. Homs-Regojo, T. N. Tran-Caliste, D. Carbone, V. L. R. Jacques, R. Grifone, P. Boesecke, J. Katzer, I. Costina, H. Djazouli, T. Schroeder and T. U. Schülli

Synopsis: A new quick continuous mapping technique that comes together with a software package (XSOCS) for automatic data analysis for strain and lattice orientation is presented as a novel type of scanning probe microscope.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 770-779  [ doi:10.1107/S1600576714004476 ]

Crystallographic study of grain refinement of Al by Nb addition

F. Wang, D. Qiu, Z.-L. Liu, J. A. Taylor, M. A. Easton and M.-X. Zhang

Synopsis: Using the edge-to-edge matching model, electron backscatter diffraction and transmission electron microscopy, good crystallographic matching and reproducible orientation relationships have been identified between refined Al grains and in situ formed pro-peritectic Al3Nb particles. These particles are therefore suggested to account for the considerable grain refinement in the Al alloys with addition of Nb solute.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 780-787  [ doi:10.1107/S1600576714004956 ]

Phase-sensitive small-angle neutron scattering

C. F. Majkrzak, K. Krycka, S. Krueger, N. F. Berk, P. Kienzle and B. Maranville

Synopsis: A method is proposed for determining the scattering length density distribution of a molecular-scale object directly from phase-sensitive small-angle neutron scattering. The structure factor amplitude is obtained through the use of a reference structure for a collection of randomly oriented, identical objects in the dilute solution limit.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 788-798  [ doi:10.1107/S1600576714005020 ]

Characterization of TEMPO-oxidized cellulose nanofibers in aqueous suspension by small-angle X-ray scattering

Y. Su, C. Burger, B. S. Hsiao and B. Chu

Synopsis: The morphology, dimensions and polydispersity of cellulose nanofibers, extracted from wood pulps using the (2,2,6,6-tetramethylpiperidine-1-yl)oxyl (TEMPO)-mediated oxidation method, were characterized by the solution small-angle X-ray scattering technique. A simplified ribbon model was derived to fit the scattering profile with high quality and computational efficiency, and the fitting results were consistent with transmission electron microscopy data.

Online 28 March 2014


short communications


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J. Appl. Cryst. (2014). 47, 799-802  [ doi:10.1107/S1600576714005056 ]

High-efficiency focusing of hard X-rays exploiting the quasi-mosaic effect in a bent germanium crystal

R. Camattari, G. Paternò, A. Battelli, V. Bellucci, B. Bastie and V. Guidi

Synopsis: A germanium crystal has been bent through a grid of superficial grooves manufactured on the sample surface. High diffraction efficiency was achieved for a monochromatic X-ray beam at 150 and 300 keV and focusing capability has been demonstrated.

Online 28 March 2014


computer programs


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J. Appl. Cryst. (2014). 47, 803-805  [ doi:10.1107/S1600576714001058 ]

WinCSD: software package for crystallographic calculations (Version 4)

L. Akselrud and Y. Grin

Synopsis: The fourth version of the program package WinCSD is multi-purpose computer software for crystallographic calculations using single-crystal and powder X-ray and neutron diffraction data. WinCSD covers the complete spectrum of crystallographic calculations, including powder diffraction pattern deconvolution, crystal structure solution and refinement in 3 + d space, reconstruction of electron density from diffraction data, and graphical representation of crystallographic information.

Online 11 March 2014


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J. Appl. Cryst. (2014). 47, 806-809  [ doi:10.1107/S1600576714004427 ]

An idealized molecular geometry library for refinement of poorly behaved molecular fragments with constraints

I. A. Guzei

Synopsis: An idealized molecular geometry library has been created as a web site to be used for refinement of difficult structures with constrained fragment geometries. The library application is illustrated with a practical example.

Online 28 March 2014


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J. Appl. Cryst. (2014). 47, 810-815  [ doi:10.1107/S1600576714004737 ]

Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules

A. Hofmann and A. E. Whitten

Synopsis: MolScat is an application that computes small-angle scattering intensities from user-provided three-dimensional models. The program can fit the theoretical scattering intensities to experimental X-ray scattering data. SAFIR is a program for interactive rigid-body modelling into low-resolution shapes restored from small-angle scattering data.

Online 28 March 2014


book reviews


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J. Appl. Cryst. (2014). 47, 816-818  [ doi:10.1107/S1600576714002726 ]

Electron Crystallography. Electron Microscopy and Electron Diffraction

Online 22 February 2014


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