Journal of Applied Crystallography

Volume 42, Part 5 (October 2009)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Three-dimensional reconstructed crystal (purple), loop (yellow) and solvent (transparent pink) for a native DNA sample. Courtesy of Brockhauser, Di Michiel, McGeehan, McCarthy & Ravelli [J. Appl. Cryst. (2008), 41, 1057-1066].

research papers


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J. Appl. Cryst. (2009). 42, 749-757  [ doi:10.1107/S0021889809024856 ]

Characterization of image plates for neutron diffraction

C. Wilkinson, M. S. Lehmann, F. Meilleur, M. P. Blakeley, D. A. A. Myles, S. Vogelmeier, M. Thoms, M. Walsh and G. J. McIntyre

Synopsis: The overall gain and point-spread function of an image-plate detector system can be determined online from single-crystal diffraction patterns to facilitate unbiased estimation of the true standard deviations of the observed integrated intensities of the Bragg reflections.

Online 1 August 2009


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J. Appl. Cryst. (2009). 42, 758-767  [ doi:10.1107/S0021889809030349 ]

Elastic deformations in a perfect bulk Si crystal studied by high-energy X-rays

A. Gröschel, H. Grillenberger and A. Magerl

Synopsis: Comparison of finite element analysis with high-energy X-ray diffraction measurements demonstrates the possibility of extracting the gradation of long-range strain fields in massive high-quality single crystals like silicon from the measured Bragg intensities.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 768-775  [ doi:10.1107/S0021889809025503 ]

Advances in powder diffraction pattern indexing: N-TREOR09

A. Altomare, G. Campi, C. Cuocci, L. Eriksson, C. Giacovazzo, A. Moliterni, R. Rizzi and P.-E. Werner

Synopsis: A new approach is described for indexing a powder pattern and determining the extinction group. A new figure of merit is also given.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 776-782  [ doi:10.1107/S0021889809026636 ]

Re-evaluation of formulae for X-ray stress analysis in polycrystalline specimens with fibre texture: experimental confirmation

R. Yokoyama, J. Harada and Y. Akiniwa

Synopsis: An X-ray diffraction measurement was performed by using a TiN thin-film specimen with [111] fibre texture, in order to see whether a profile of the 420 X-ray reflection changes or not depending on the biaxial load. The results obtained by this examination agree quantitatively with a theoretical prediction.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 783-792  [ doi:10.1107/S0021889809025461 ]

Models of uniformity for grain boundary distributions

A. Morawiec

Synopsis: Models of uniformity needed for defning statistical grain boundary density functions are discussed. It is proposed to use some models derived from an assumed metric of grain boundary space.

Online 1 August 2009


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J. Appl. Cryst. (2009). 42, 793-797  [ doi:10.1107/S0021889809023589 ]

Theoretical analysis of apical bonding in copper(II) chelates with amino acids

A. Milicevic and N. Raos

Synopsis: The apical ligand is bonded at the sterically more crowded side of a complex, and apical bond length shows sigmoidal dependence on distortion of the coordination polyhedron.

Online 1 August 2009


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J. Appl. Cryst. (2009). 42, 798-809  [ doi:10.1107/S0021889809024376 ]

Handling cell-parameter errors in crystallographic data

J. Haestier

Synopsis: Cell-error effects on crystallographic data and on derived parameters are reviewed. New algorithms are presented for more efficient error handling.

Online 1 August 2009


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J. Appl. Cryst. (2009). 42, 810-814  [ doi:10.1107/S0021889809025138 ]

Finding crystal structures of peptides by random search and evolutionary algorithms

A. Immirzi, L. Erra and C. Tedesco

Synopsis: The computer program PTRY has been devised to perform X-ray structural studies of crystalline peptides when only limited diffraction data are available. It is based on a random search in the internal-coordinate space and evolutionary algorithms.

Online 8 August 2009


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J. Appl. Cryst. (2009). 42, 815-819  [ doi:10.1107/S0021889809023310 ]

In situ monitoring by synchrotron radiation of the formation of ZnO nanoparticles by aqueous chemical growth

S. Fall, O. Konovalov, M. Maaza, A. C. Beye and A. Gibaud

Synopsis: An in situ synchrotron radiation grazing-incidence diffraction study is presented of the kinetics of the formation of nanoparticles of ZnO grown by the aqueous chemical growth technique.

Online 8 August 2009


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J. Appl. Cryst. (2009). 42, 820-833  [ doi:10.1107/S0021889809028064 ]

AMPLIMODES: symmetry-mode analysis on the Bilbao Crystallographic Server

D. Orobengoa, C. Capillas, M. I. Aroyo and J. M. Perez-Mato

Synopsis: AMPLIMODES is a computer program available on the Bilbao Crystallographic Server that can perform a symmetry-mode analysis of any distorted structure of displacive type.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 834-845  [ doi:10.1107/S0021889809023218 ]

Experimental and theoretical study of the diffraction properties of various crystals for the realization of a soft gamma-ray Laue lens

N. Barrière, J. Rousselle, P. von Ballmoos, N. V. Abrosimov, P. Courtois, P. Bastie, T. Camus, M. Jentschel, V. N. Kurlov, L. Natalucci, G. Roudil, N. Frisch Brejnholt and D. Serre

Synopsis: This paper describes the development of efficient crystals for a Laue lens application. The theoretical study aimed to identify the crystals, either pure or two-component crystals, best suited to this application and three different materials were then characterized experimentally.

Online 1 August 2009


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J. Appl. Cryst. (2009). 42, 846-866  [ doi:10.1107/S0021889809027897 ]

Phase behaviour and thermoelastic properties of perdeuterated ammonia hydrate and ice polymorphs from 0 to 2 GPa

A. D. Fortes, I. G. Wood, L. Vocadlo, K. S. Knight, W. G. Marshall, M. G. Tucker and F. Fernandez-Alonso

Synopsis: This paper reports neutron powder diffraction studies of ammonia dihydrate up to 2 GPa, including identification of new high-pressure polymorphs and measurement of their equations of state. Data for co-existing water ice and ammonia monohydrate polymorphs are also reported.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 867-877  [ doi:10.1107/S0021889809023541 ]

A combined fit of total scattering and extended X-ray absorption fine structure data for local-structure determination in crystalline materials

V. Krayzman, I. Levin, J. C. Woicik, Th. Proffen, T. A. Vanderah and M. G. Tucker

Synopsis: Extended X-ray absorption fine structure (EXAFS) data were included in simultaneously fitted experimental data for the reverse Monte Carlo refinement of local atomic structure using the public domain software RMCProfile. Structural refinements of complex perovskites demonstrated that inclusion of the EXAFS data provided the constraints necessary to recover fine details of the local atomic arrangements.

Online 1 August 2009


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J. Appl. Cryst. (2009). 42, 878-884  [ doi:10.1107/S0021889809025709 ]

Conoscopic method for determination of main refractive indices and thickness of a uniaxial crystal cut out parallel to its optical axis

L. Dumitrascu, I. Dumitrascu and D. O. Dorohoi

Synopsis: A simplified data acquisition and analysis technique, for determining the main refractive indices and the thickness of a uniaxial anisotropic crystal cut out parallel with the optical axis by digitally processing the conoscopic interference figures, is presented.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 885-891  [ doi:10.1107/S0021889809030921 ]

A comparison of a microfocus X-ray source and a conventional sealed tube for crystal structure determination

T. Schulz, K. Meindl, D. Leusser, D. Stern, J. Graf, C. Michaelsen, M. Ruf, G. M. Sheldrick and D. Stalke

Synopsis: Experiments are described in which a direct comparison was made between a conventional sealed tube and a microfocus X-ray source with multilayer optics. They reveal the latter to be far superior for the investigation of small crystals.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 892-900  [ doi:10.1107/S0021889809029288 ]

Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamline

G. David and J. Pérez

Synopsis: A prototype was developed to perform online purification and automatic loading of protein solutions at a small-angle X-ray scattering beamline.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 901-905  [ doi:10.1107/S0021889809027873 ]

A fast X-ray chopper for single-bunch extraction at synchrotron sources

A. Meents, B. Reime, M. Kaiser, X.-Y. Wang, R. Abela, E. Weckert and C. Schulze-Briese

Synopsis: A newly developed fast mechanical X-ray chopper provides an opening time of 230 ns and an excellent long-term jitter of less than 3 ns.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 906-916  [ doi:10.1107/S0021889809028374 ]

Round robin on Rietveld quantitative phase analysis of Portland cements

L. León-Reina, A. G. De la Torre, J. M. Porras-Vázquez, M. Cruz, L. M. Ordonez, X. Alcobé, F. Gispert-Guirado, A. Larrañaga-Varga, M. Paul, T. Fuellmann, R. Schmidt and M. A. G. Aranda

Synopsis: An interlaboratory study on artificial and commercial Portland clinker and cements has allowed the reproducibility and uncertainty ranges for the components to be established.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 917-924  [ doi:10.1107/S0021889809031021 ]

Nonstoichiometry, amorphicity and microstructural evolution during phase transformations of photocatalytic titania powders

S. H. Lim, C. Ritter, Y. Ping, M. Schreyer and T. J. White

Synopsis: Fixed-wavelength neutron and multiple-wavelength X-ray powder diffraction are used to assess phase development in alkoxide-derived titania gel as a function of temperature.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 925-931  [ doi:10.1107/S0021889809029422 ]

Characterization of the hierarchical structures of a dry nanopowder in a polymer matrix by X-ray scattering techniques

M. C. Kane, J. D. Londono, F. L. Beyer and A. B. Brennan

Synopsis: The degree of agglomeration of epoxy-TiO2 nanocomposites is elucidated by the combined use of X-ray scattering and microscopy.

Online 16 September 2009


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J. Appl. Cryst. (2009). 42, 932-943  [ doi:10.1107/S0021889809032919 ]

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules

J. Bardhan, S. Park and L. Makowski

Synopsis: An accurate numerical approach has been implemented for calculating wide-angle X-ray solution scattering patterns of proteins using the traditional scattering model that treats water as a continuum. The results suggest that, at wide angles, the excluded-volume and solvation-layer contributions to scattering cannot be reliably estimated using the continuum representation.

Online 8 September 2009


cryocrystallography papers


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J. Appl. Cryst. (2009). 42, 944-952  [ doi:10.1107/S0021889809023553 ]

Slow cooling of protein crystals

M. Warkentin and R. E. Thorne

Synopsis: High-quality, ice-free X-ray diffraction data were continuously collected while cryoprotectant-free thaumatin crystals were cooled at 0.1 K s-1 from 300 to 100 K. This establishes the feasibility of fully temperature controlled studies of protein structure and dynamics, and provides insight into how cooling creates crystal disorder.

Online 1 August 2009


computer programs


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J. Appl. Cryst. (2009). 42, 953-958  [ doi:10.1107/S0021889809034062 ]

SMEPOC - a computer program for the automatic generation of trial structural models for inorganic compounds with symmetry restriction

X. Deng and C. Dong

Synopsis: An algorithm and the corresponding program SMEPOC have been developed for automatic generation of trial structures for inorganic compounds from the unit-cell content and the space-group information.

Online 8 September 2009


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J. Appl. Cryst. (2009). 42, 959-964  [ doi:10.1107/S0021889809023863 ]

BioXTAS RAW, a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis

S. S. Nielsen, K. N. Toft, D. Snakenborg, M. G. Jeppesen, J. K. Jacobsen, B. Vestergaard, J. P. Kutter and L. Arleth

Synopsis: BioXTAS RAW is a fully open source software program for automated two-dimensional and one-dimensional data reduction and preliminary analysis of isotropic small-angle X-ray scattering data.

Online 8 August 2009


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J. Appl. Cryst. (2009). 42, 965-974  [ doi:10.1107/S0021889809025746 ]

PolySNAP3: a computer program for analysing and visualizing high-throughput data from diffraction and spectroscopic sources

G. Barr, W. Dong and C. J. Gilmore

Synopsis: PolySNAP3 is a computer program for the classification of powder diffraction, spectroscopic and numerical data either separately or combined.

Online 8 August 2009


laboratory notes


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J. Appl. Cryst. (2009). 42, 975-976  [ doi:10.1107/S0021889809028805 ]

A simple technique to convert sitting-drop vapor diffusion into hanging-drop vapor diffusion by solidifying the reservoir solution with agarose

T. W. Whon, Y.-H. Lee, D.-S. An, H. K. Song and S.-G. Kim

Synopsis: Solidification of the reservoir solution with agarose allows an upside-down sitting-drop plate to be used in a hanging-drop vapor-diffusion crystallization method.

Online 8 September 2009


 

J. Appl. Cryst. (2009). 42, 977-980

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