Journal of Applied Crystallography

Volume 41, Part 2 (April 2008)



[Issue Author Index][Volume Author Index]
[Cover 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


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J. Appl. Cryst. (2008). 41, 237-248  [ doi:10.1107/S0021889808000617 ]

Evaluation of the focusing performance of bent Laue crystals using wave-optical theory

Y. I. Nesterets and S. W. Wilkins

Synopsis: Quantitative analysis of the focusing performance of bent Laue crystals is carried out using numerical solution of the Takagi equations and the Fresnel integral. In addition, a formula for the geometrical aberration of a cylindrically bent crystal is derived.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 249-251  [ doi:10.1107/S0021889808000514 ]

Incorporation of a new design of backing seat and anvil in a Merrill-Bassett diamond anvil cell

S. A. Moggach, D. R. Allan, S. Parsons and J. E. Warren

Synopsis: A modification to the Merrill-Bassett diamond anvil cell is presented. This design incorporates tungsten carbide backing disks and Boehler-Almax-cut diamonds which permit the full opening angle, and maximum pressure attainable to remain comparable with the previous backing seat and anvil design, whilst removing troublesome beryllium.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 252-261  [ doi:10.1107/S0021889808000277 ]

Small-angle X-ray scattering study of intramuscular fish bone: collagen fibril superstructure determined from equidistant meridional reflections

C. Burger, H. Zhou, I. Sics, B. S. Hsiao, B. Chu, L. Graham and M. J. Glimcher

Synopsis: Small-angle equidistant meridional reflections from intramuscular shad/herring bone were analyzed on the basis of a two-dimensional fitting scheme that takes preferred orientation effects into account.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 262-271  [ doi:10.1107/S0021889808001064 ]

Simulating X-ray diffraction of textured films

D. W. Breiby, O. Bunk, J. W. Andreasen, H. T. Lemke and M. M. Nielsen

Synopsis: Computer simulations of grazing-incidence X-ray diffraction measurements of textured films are outlined.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 272-280  [ doi:10.1107/S0021889808001167 ]

Evidence of stacking-fault distribution along an InAs nanowire using micro-focused coherent X-ray diffraction

V. Chamard, J. Stangl, S. Labat, B. Mandl, R. T. Lechner and T. H. Metzger

Synopsis: InAs nanowires that exhibit a significant amount of wurtzite structure have been investigated using phase-sensitive coherent X-ray diffraction with a micro-focused beam at a synchrotron source. Simulations compared with experiments evidence the presence of stacking faults distributed along the wire.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 281-291  [ doi:10.1107/S0021889808001271 ]

Polystyrene-b-polyisoprene thin films with hexagonally perforated layer structure: quantitative grazing-incidence X-ray scattering analysis

K. Heo, J. Yoon, S. Jin, J. Kim, K.-W. Kim, T. J. Shin, B. Chung, T. Chang and M. Ree

Synopsis: Grazing-incidence X-ray scattering formulas were derived for hexagonally perforated layer systems with ABC and AB stacking sequences in substrate-supported nanoscale thin films. Using these formulas the GIXS data obtained for polystyrene-b-polyisoprene thin films supported on silicon substrates were quantitatively analyzed, providing information about the structural parameters, perforated layer stacking sequence and orientation of the films.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 292-301  [ doi:10.1107/S0021889808001520 ]

Ab initio structure determination of a pharmaceutical compound, prednisolone succinate, from synchrotron powder data by combination of a genetic algorithm and the maximum entropy method

E. Nishibori, T. Ogura, S. Aoyagi and M. Sakata

Synopsis: An accurate structure of a mid-sized pharmaceutical compound, prednisolone succinate, has been determined using high-resolution powder data collected at SPring-8 by a newly developed analytical method, which is a combination of a genetic algorithm and the maximum entropy method. The analytical procedures are described in detail.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 302-309  [ doi:10.1107/S0021889808001684 ]

X-ray diffraction contrast tomography: a novel technique for three-dimensional grain mapping of polycrystals. I. Direct beam case

W. Ludwig, S. Schmidt, E. M. Lauridsen and H. F. Poulsen

Synopsis: A nondestructive tomographic imaging technique revealing simultaneously the grain and the absorption microstructure of undeformed polycrystalline materials is described.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 310-318  [ doi:10.1107/S0021889808001726 ]

X-ray diffraction contrast tomography: a novel technique for three-dimensional grain mapping of polycrystals. II. The combined case

G. Johnson, A. King, M. G. Honnicke, J. Marrow and W. Ludwig

Synopsis: An extension to the nondestructive tomographic imaging technique revealing simultaneously the grain and the absorption microstructure of undeformed polycrystalline materials is described. The technique uses simultaneous acquisition of direct and diffracted beams.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 319-328  [ doi:10.1107/S0021889808001672 ]

Optimal side-chain packing in proteins and crystallographic refinement

S. Gore and T. Blundell

Synopsis: An optimal side-chain placement algorithm is adapted to protein crystallographic refinement. Its utility is evaluated for single/multi-conformer refinement and sequence-registry identification.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 329-339  [ doi:10.1107/S0021889808002732 ]

Molecular envelopes derived from protein powder diffraction data

J. P. Wright, C. Besnard, I. Margiolaki, S. Basso, F. Camus, A. N. Fitch, G. C. Fox, P. Pattison and M. Schiltz

Synopsis: The feasibility of low-resolution phasing via the single isomorphous replacement method from protein powder data is demonstrated.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 340-349  [ doi:10.1107/S0021889808004482 ]

Optimization and evaluation of data quality for charge density studies

V. V. Zhurov, E. A. Zhurova and A. A. Pinkerton

Synopsis: Criteria for the evaluation of hardware and software for charge density studies and evaluation of area-detector data are presented.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 350-355  [ doi:10.1107/S0021889808003245 ]

Modified design and use of a high-pressure environmental stage for laboratory X-ray powder diffractometers

P. S. Whitfield, A. V. Nawaby, B. Blak and J. Ross

Synopsis: A high-pressure chamber for conducting laboratory X-ray powder diffraction experiments up to 12.4 MPa has been modified from an existing design. Changes were made to meet current design codes (ASME 31.3), and finite element analysis revealed that thinner Be windows than previously thought could safely be used.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 356-362  [ doi:10.1107/S0021889807066745 ]

Surface morphology of sputtered Ta2O5 thin films on Si substrates from X-ray reflectivity at a fixed angle

H.-Y. Lee, T.-W. Huang, C.-H. Lee and Y.-W. Hsieh

Synopsis: The temporal variation of the surface morphology of Ta2O5 films on Si substrates has been measured using X-ray reflectivity at a fixed angle during radio-frequency magnetron sputtering. During an early stage of growth of polycrystalline Ta2O5, the variation of surface roughness revealed a morphology of island nucleation and island coalescence.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 363-365  [ doi:10.1107/S0021889807067787 ]

Molecular axes and planes as an Eigenvalue problem

D.-M. Smilgies

Synopsis: A statistical approach is used to define the long molecular axis and the main molecular plane. From the molecular axes and planes, the orientation of the molecule with respect to the lattice as well as intermolecular orientations can be characterized.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 366-372  [ doi:10.1107/S0021889807068094 ]

High-resolution X-ray diffraction in situ study of very small complexes: the case of hydrogenated dilute nitrides

G. Bisognin, D. De Salvador, E. Napolitani, M. Berti, A. Polimeni, M. Capizzi, S. Rubini, F. Martelli and A. Franciosi

Synopsis: This paper describes the use of in situ high-resolution X-ray diffraction measurements using a conventional laboratory source for the study of the evolution kinetics of very small complexes under annealing.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 373-376  [ doi:10.1107/S0021889808004652 ]

Convenient off-line error quantification and characterization of concentricity of two circles of rotation for diffractometer alignment

L. M. D. Cranswick, R. Donaberger, I. P. Swainson and Z. Tun

Synopsis: To ensure concentricity of the [theta]-2[theta] rotation stages, but with a very limited 2[theta] range of rotation, an alignment technique using two dial gauges mounted at right angles to each other (X and Y axes) is described.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 377-385  [ doi:10.1107/S0021889807066836 ]

X-ray diffraction at constant penetration depth - a viable approach for characterizing steep residual stress gradients

T. Erbacher, A. Wanner, T. Beck and O. Vöhringer

Synopsis: The feasibility of a new experimental approach for characterizing the strongly graded, non-equiaxed stress state existing at a machined surface is demonstrated. The results from constant-penetration-depth measurements on the ground surface of an engineering ceramic are compared with those from conventional sin2[psi] measurements.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 386-392  [ doi:10.1107/S0021889807067131 ]

Determination of B-cation chemical short-range order in perovskites from the total pair-distribution function

V. Krayzman and I. Levin

Synopsis: Two distinct methods are compared for the determination of the B-cation chemical short-range order (SRO) parameters from the total scattering pair-distribution function. One of the approaches, which proved to yield the most accurate results, was used to analyze the SRO of Ti and Zr in powder samples of Ca(Zr,Ti)O3.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 393-401  [ doi:10.1107/S0021889807067659 ]

New measures of sharpness for symmetric powder diffraction peak profiles

T. Ida

Synopsis: New measures of sharpness for symmetric powder diffraction peak profiles are proposed. Analytical expressions for typical model profile functions and theoretical size-broadening profiles with statistical size distribution are presented.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 402-415  [ doi:10.1107/S0021889808004202 ]

Structural characterization of the clay mineral illite-1M

A. F. Gualtieri, S. Ferrari, M. Leoni, G. Grathoff, R. Hugo, M. Shatnawi, G. Paglia and S. Billinge

Synopsis: This work presents the structural characterization of illite-1M from northern Hungary using state-of-the-art analytical methods available for clays. This is the first attempt to refine the structure model and locate the interlayer water molecule in this clay mineral species.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 416-427  [ doi:10.1107/S0021889808000733 ]

Quantitative characterization of the contrast mechanisms of ultra-small-angle X-ray scattering imaging

F. Zhang, G. G. Long, L. E. Levine, J. Ilavsky and P. R. Jemian

Synopsis: The contrast mechanism of ultra-small-angle X-ray scattering imaging is explained based on phase propagation and dynamical diffraction theory. A complementary geometrical analysis is also presented.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 428-435  [ doi:10.1107/S0021889808004792 ]

Non-ambient X-ray diffraction residual stress analysis of thin films: tracing nanosize-related effects on thermoelastic constants and identifying sources of residual stresses

Y. Kuru, M. Wohlschlögel, U. Welzel and E. J. Mittemeijer

Synopsis: Pitfalls during non-ambient X-ray diffraction stress analysis of thin films (with nanosized grains) are discussed. Recipes for identifying nanosize-related effects on thermoelastic constants and various sources of residual stresses are provided.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 436-445  [ doi:10.1107/S0021889808004937 ]

Simultaneous estimation of the form factor and structure factor for globular particles in small-angle scattering

S. Hansen

Synopsis: Small-angle scattering data from non-dilute solutions of globular particles are analysed by indirect Fourier transformation without the use of a specific model structure factor.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 446-455  [ doi:10.1107/S0021889808004846 ]

Distorted f.c.c. arrangement of gold nanoclusters: a model of spherical particles with microstrains and stacking faults

A. Longo and A. Martorana

Synopsis: A model of distorted f.c.c. arrangement for silica-supported gold nanoclusters brings about satisfactory fitting to X-ray diffraction data and is confirmed by EXAFS analysis. Using ordered f.c.c. and noncrystalline (icosahedral and decahedral) components, the X-ray diffraction fitting is also good, but the results are in contrast to EXAFS data.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 456-465  [ doi:10.1107/S0021889808004950 ]

Small-angle neutron scattering and the errors in protein structures that arise from uncorrected background and intermolecular interactions

K. A. Rubinson, C. Stanley and S. Krueger

Synopsis: Making a complete background correction for SANS from solutions of biological macromolecules enables more accurate values for the calculated shapes and sizes of the molecules and leads to valid interpretations of solvation as well as the magnitudes of intermolecular interactions.

Online 8 March 2008


computer programs


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J. Appl. Cryst. (2008). 41, 466-470  [ doi:10.1107/S0021889807067908 ]

Mercury CSD 2.0 - new features for the visualization and investigation of crystal structures

C. F. Macrae, I. J. Bruno, J. A. Chisholm, P. R. Edgington, P. McCabe, E. Pidcock, L. Rodriguez-Monge, R. Taylor, J. van de Streek and P. A. Wood

Synopsis: The Materials Module of Mercury is introduced, which includes functionality to search the Cambridge Structural Database for packing motifs and to perform structure-similarity calculations. Further new features within Mercury CSD 2.0 include links to IsoStar and ConQuest, visualization of voids and image output to the program POV-Ray.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 471-475  [ doi:10.1107/S0021889808000381 ]

A cyberenvironment for crystallography and materials science and an integrated user interface to the Crystallography Open Database and Predicted Crystallography Open Database

J. R. Fennick, J. B. Keith, R. H. Leonard, T. N. Truong and J. P. Lewis

Synopsis: The Computational Science and Engineering Online (CSE-Online) environment provides various tools and services to crystallographic computing illustrated by an interface to the Crystallography Open Database and Predicted Crystallography Open Database.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 476-478  [ doi:10.1107/S0021889808001647 ]

CAIROTEP: ORTEPIII incorporating CAIRO for better outputs

Y. Lin

Synopsis: ORTEPIII has been adapted to incorporate the CAIRO graphics back-end to improve the output quality and program usability. A simple Python helper for instruction file generation, CIFTEP, is also provided.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 479-480  [ doi:10.1107/S0021889808003415 ]

Program CRYC3D for geometric computing in crystallography

L. Urzhumtseva and A. Urzhumtsev

Synopsis: The computer program CRYC3D has been developed as a convenient and user-friendly way of calculating basic geometric characteristics of three-dimensional crystallographic objects.

Online 8 March 2008


laboratory notes


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J. Appl. Cryst. (2008). 41, 481-482  [ doi:10.1107/S0021889808000861 ]

DiXP: a Python-based GUI for controlling a powder diffractometer via the Internet

Z. Izaola and G. Madariaga

Synopsis: DiXP is a multi-platform open source software that allows the remote control of an X-ray powder diffractometer through the Internet. Its implementation using Python and a client/server architecture make this program of widespread purpose and straightforward generalization.

Online 8 March 2008


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J. Appl. Cryst. (2008). 41, 483-486  [ doi:10.1107/S0021889808000952 ]

Microcrystal screening with a novel design for beamline-mountable crystallization wells

C. S. Lunde, S. Rouhani, J. P. Remis and R. M. Glaeser

Synopsis: A simple and flexible system is described for in situ screening of microcrystals of membrane proteins that are grown within a connected-bilayer matrix formed by hydrated lipids. Crystallization wells can be individually excised and mounted for diffraction screening on a synchrotron X-ray source.

Online 8 March 2008


book reviews


 

[HTML version][PDF version]  [Open access]

J. Appl. Cryst. (2008). 41, 487  [ doi:10.1107/S0021889808002355 ]

Random fields and spin glasses: a field theory approach

Online 8 March 2008


 

J. Appl. Cryst. (2008). 41, 488-490

forthcoming meetings and short courses


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