Journal of Applied Crystallography

Volume 42, Part 2 (April 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, 153-160  [ doi:10.1107/S0021889809002040 ]

Phase relations in the Ba-Sr-Co-Fe-O system at 1273 K in air

Z. Yáng, A. S. Harvey, A. Infortuna and L. J. Gauckler

Synopsis: An isothermal phase map for the Ba-Sr-Co-Fe-O system is proposed.

Online 3 February 2009


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J. Appl. Cryst. (2009). 42, 161-168  [ doi:10.1107/S0021889809002854 ]

Small-angle neutron scattering study of the miscibility of metallocene-catalyzed octene linear low-density polyethylene and low-density polyethylene blends

T. J. Shin, B. Lee, J. Lee, S. Jin, B. S. Sung, Y. S. Han, C.-H. Lee, R. S. Stein and M. Ree

Synopsis: The miscibility of octene-mLLDPE(D)/LDPE(H) blends was studied with small-angle neutron and X-ray scattering techniques. It was found that the blends are miscible in both the melt and the quenched states, and two polymer components are cocrystallized via fast crystallization from the melt state.

Online 7 February 2009


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J. Appl. Cryst. (2009). 42, 169-173  [ doi:10.1107/S0021889809002751 ]

Predicting the quaternary structure attribute of a protein by hybridizing functional domain composition and pseudo amino acid composition

X. Xiao, P. Wang and K.-C. Chou

Synopsis: A user friendly web server, called PQSA-Pred, has been established at http://218.65.61.89:8080/bioinfo/pqsa-pred, by which one can predict the quaternary structural attributes of proteins according to their sequence information alone.

Online 14 February 2009


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J. Appl. Cryst. (2009). 42, 174-178  [ doi:10.1107/S0021889809003227 ]

An approach to high-throughput X-ray diffraction analysis of combinatorial polycrystalline thin film libraries

S. Roncallo, O. Karimi, K. D. Rogers, D. W. Lane and S. A. Ansari

Synopsis: An initial report is presented of a high-throughput X-ray diffraction method, combining simultaneous data collection of multiple diffraction patterns with the electronic partitioning required to calculate lattice parameter information for the individual samples.

Online 27 February 2009


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J. Appl. Cryst. (2009). 42, 179-184  [ doi:10.1107/S0021889809004981 ]

Bond valence sum: a new soft chemical constraint for RMCProfile

S. T. Norberg, M. G. Tucker and S. Hull

Synopsis: The implementation and demonstration of a soft chemical constraint, based on bond valence calculations, for the reverse Monte Carlo program RMCProfile is reported.

Online 27 February 2009


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J. Appl. Cryst. (2009). 42, 185-191  [ doi:10.1107/S0021889809003409 ]

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

R. Yokoyama and J. Harada

Synopsis: The stress-strain relation used in X-ray stress analysis for polycrystalline specimens with fibre texture is re-examined by taking into account the symmetry of the reciprocal lattice (Laue class) of the constituent crystallites. The treatment is applicable to any polycrystalline specimen in any Laue class.

Online 5 March 2009


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J. Appl. Cryst. (2009). 42, 192-197  [ doi:10.1107/S0021889809004300 ]

Formalism for the determination of intermediate stress gradients using X-ray diffraction

T. Gnäupel-Herold

Synopsis: This work presents angle calculations necessary for orienting line-shaped beam spots and for calculating effective azimuth and tilt angles for residual stress determination in a four-circle goniometer.

Online 5 March 2009


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J. Appl. Cryst. (2009). 42, 198-210  [ doi:10.1107/S0021889809005135 ]

Comparative X-ray diffraction study of the crystalline microstructure of tetragonal and monoclinic vanadium-zirconium dioxide solid solutions produced from gel precursors

M. A. Kojdecki, E. Ruiz de Sola, F. J. Serrano, J. M. Amigó and J. Alarcón

Synopsis: Thermal treatment of gel precursors with initial compositions VxZr1-xO2 (0 [less-than or equal to] x [less-than or equal to] 0.1), with a final annealing temperature of 723 or 1573 K, resulted in a major tetragonal or pure monoclinic zirconia phase. Each pure or vanadium-doped zirconia specimen is characterized by a prevalent crystallite shape, a volume-weighted crystallite size distribution and a second-order crystalline lattice strain distribution.

Online 14 March 2009


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J. Appl. Cryst. (2009). 42, 211-216  [ doi:10.1107/S0021889809007171 ]

Diffraction features due to ordered distribution of twin boundaries in orthorhombic Ni-Mn-Ga crystals

A. Ustinov, L. Olikhovska, N. Glavatska and I. Glavatskyy

Synopsis: The intensity distributions from an orthorhombic single crystal containing twin boundaries (110), <1{\overline 1}0> that tend to short-range order were simulated in the reciprocal lattice space using Monte Carlo techniques.

Online 14 March 2009


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J. Appl. Cryst. (2009). 42, 217-224  [ doi:10.1107/S0021889809003483 ]

Optimization of focusing neutronic devices using artificial intelligence techniques

P. M. Bentley and K. H. Andersen

Synopsis: The design and optimization of focusing neutron guide elements using swarm intelligence are described. A large gain in performance is observed compared with the best human designs for complex devices.

Online 14 February 2009


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J. Appl. Cryst. (2009). 42, 225-233  [ doi:10.1107/S0021889809005810 ]

The ikaite-to-vaterite transformation: new evidence from diffraction and imaging

C. C. Tang, S. P. Thompson, J. E. Parker, A. R. Lennie, F. Azough and K. Kato

Synopsis: The ikaite-vaterite transformation was observed in polycrystalline samples during dehydration. Although the original ikaite morphology is retained following dehydration, development of domain structure is observed in individual crystallites. A structural model is developed to describe the transformation to vaterite.

Online 27 February 2009


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J. Appl. Cryst. (2009). 42, 234-241  [ doi:10.1107/S0021889809001654 ]

Determination of crystal phase from an electron backscatter diffraction pattern

D. J. Dingley and S. I. Wright

Synopsis: A novel method for extracting the crystal symmetry and unit-cell parameters from electron backscatter diffraction patterns is described.

Online 24 January 2009


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J. Appl. Cryst. (2009). 42, 242-252  [ doi:10.1107/S0021889808042131 ]

Odd electron diffraction patterns in silicon nanowires and silicon thin films explained by microtwins and nanotwins

C. Cayron, M. Den Hertog, L. Latu-Romain, C. Mouchet, C. Secouard, J.-L. Rouviere, E. Rouviere and J.-P. Simonato

Synopsis: Anomalous extra spots visible in electron diffraction patterns of silicon nanowires and silicon thin films are explained by the presence of micro- and nanotwins.

Online 24 January 2009


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J. Appl. Cryst. (2009). 42, 253-258  [ doi:10.1107/S002188980804332X ]

Negative (and very low) thermal expansion in ReO3 from 5 to 300 K

M. Dapiaggi and A. N. Fitch

Synopsis: The very small negative thermal expansion of ReO3 below room temperature has been confirmed from careful high-resolution powder diffraction measurements. The systematic errors that can arise when using synchrotron radiation for such studies are considered.

Online 3 February 2009


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J. Appl. Cryst. (2009). 42, 259-264  [ doi:10.1107/S0021889809003094 ]

Combining solution wide-angle X-ray scattering and crystallography: determination of molecular envelope and heavy-atom sites

X. Hong and Q. Hao

Synopsis: Molecular envelopes determined from SAXS/WAXS solution scattering can be used to locate the heavy-atom sites in the crystallographic unit cell.

Online 7 February 2009


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J. Appl. Cryst. (2009). 42, 265-267  [ doi:10.1107/S0021889809003987 ]

Observation of light-induced localized domain-inversion pattern formation in KNbO3

Y. Chen, Z. Lu and M. Xiao

Synopsis: It is demonstrated that high-intensity illumination with an Ar-ion laser beam can generate domain-inversion patterning in KNbO3 crystals.

Online 14 February 2009


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J. Appl. Cryst. (2009). 42, 268-278  [ doi:10.1107/S0021889809002544 ]

The Fourier transforms of curves and filaments and their application to low-resolution protein crystallography

A. C. Hausrath and A. Goriely

Synopsis: A numerical method for the evaluation of the Fourier transform of a general space curve is described and its application to low-resolution crystallographic data analysis is presented.

Online 14 February 2009


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J. Appl. Cryst. (2009). 42, 279-283  [ doi:10.1107/S0021889809003446 ]

Agarose gel facilitates enzyme crystal soaking with a ligand analog

C. Sauter, C. Balg, A. Moreno, K. Dhouib, A. Théobald-Dietrich, R. Chênevert, R. Giegé and B. Lorber

Synopsis: Agarose gel stabilizes the AspRS enzyme crystal lattice for soaking with a catalytic intermediate analog. By contrast, AspRS crystals prepared in solution broke apart within 10-30 s after the ligand was introduced into the mother liquor, and subsequently these fragments became an amorphous precipitate.

Online 14 February 2009


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J. Appl. Cryst. (2009). 42, 284-294  [ doi:10.1107/S0021889809004269 ]

Structural and thermal properties of the monoclinic Lu2SiO5 single crystal: evaluation as a new laser matrix

H. Cong, H. Zhang, J. Wang, W. Yu, J. Fan, X. Cheng, S. Sun, J. Zhang, Q. Lu, C. Jiang and R. I. Boughton

Synopsis: The novel laser matrix Lu2SiO5 (LSO) presents a structure consisting of two interpenetrating frameworks, Lu1O6 and Lu2O7. The material shows a maximum thermal expansion of 10.1105 × 10-6 K and thermal conductivity of 3.67 W m-1 K-1 at 303.15 K, while exhibiting relatively large anisotropic thermal properties.

Online 27 February 2009


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J. Appl. Cryst. (2009). 42, 295-301  [ doi:10.1107/S0021889809004713 ]

Direct mapping of fiber diffraction patterns into reciprocal space

N. Stribeck and U. Nöchel

Synopsis: For application in time-resolved wide-angle X-ray diffraction studies, a method for the automatic mapping of fiber diffraction patterns into reciprocal space has been designed.

Online 27 February 2009


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J. Appl. Cryst. (2009). 42, 302-307  [ doi:10.1107/S0021889809004051 ]

Crystal structure solution of small-to-medium-sized molecules at non-atomic resolution

R. Caliandro, B. Carrozzini, G. L. Cascarano, C. Giacovazzo, A. Mazzone and D. Siliqi

Synopsis: Phasing of small and medium-sized molecules is attempted at different data resolutions via different algorithms.

Online 5 March 2009


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J. Appl. Cryst. (2009). 42, 308-311  [ doi:10.1107/S0021889809006979 ]

Tilt and twist grain boundaries

A. Morawiec

Synopsis: Conditions for a planar homophase grain boundary to be concurrently a tilt and a twist boundary are given.

Online 14 March 2009


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J. Appl. Cryst. (2009). 42, 312-322  [ doi:10.1107/S0021889809007316 ]

Anomalous grazing incidence small-angle X-ray scattering of carbon-encapsulated Au and Cu clusters

J.-P. Simon, D. Babonneau, M. Drouet and O. Lyon

Synopsis: Methodologies to separate different signals in anomalous grazing incidence small-angle X-ray scattering are presented for well characterized samples: two binary nanocomposite films with Au or Cu nanoclusters encapsulated in amorphous carbon and one ternary film including both Au and Cu nanoclusters within the carbon matrix. The differential method appears the most efficient since the anomalous signal is well separated from that of the non-anomalous contributions, whatever their scattering profiles.

Online 14 March 2009


short communications


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J. Appl. Cryst. (2009). 42, 323-325  [ doi:10.1107/S0021889808042453 ]

On the determination of partial structure functions in small-angle scattering exemplified by Al89Ni6La5 alloy

A. Hoell, D. Tatchev, S. Haas, J. Haug and P. Boesecke

Synopsis: A comparison between the resonant scattering curve obtained by anomalous small-angle X-ray scattering at the X-ray absorption edge of Ni and the small-angle neutron scattering curve from an Al89Ni6La5 alloy sample is reported. It is shown that the two curves are proportional to each other and to the Ni-Ni partial structure factor.

Online 24 January 2009


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J. Appl. Cryst. (2009). 42, 326-328  [ doi:10.1107/S0021889809002143 ]

Chord length distribution of pentagonal and hexagonal rods: relation to small-angle scattering

W. Gille, N. G. Aharonyan and H. S. Harutyunyan

Synopsis: Chord length density functions and characteristic details of the small-angle scattering of infinitely long cylinders with pentagonal/hexagonal right section are analyzed.

Online 24 January 2009


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J. Appl. Cryst. (2009). 42, 329-332  [ doi:10.1107/S0021889809000077 ]

A rapid method for qu­antifying heavy atom derivatives for multiple isomorphous replacement in protein crystallography

L. A. Colip, A. T. Koppisch, R. D. Broene, J. A. Berger, S. M. Baldwin, M. N. Harris, L. J. Peterson, B. P. Warner and E. R. Birnbaum

Synopsis: A method is described for using X-ray fluorescence for determining the solution phase reaction stoichiometry of heavy atom incorporation reactions.

Online 24 January 2009


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J. Appl. Cryst. (2009). 42, 333-335  [ doi:10.1107/S0021889809001721 ]

Online collection and analysis of X-ray fluorescence spectra on the macromolecular crystallography beamlines of the ESRF

G. Leonard, V. A. Solé, A. Beteva, J. Gabadinho, M. Guijarro, J. McCarthy, D. Marrocchelli, D. Nurizzo, S. McSweeney and C. Mueller-Dieckmann

Synopsis: This paper describes the implementation of an online tool for the collection and qualitative analysis of X-ray fluorescence spectra that allows the identification of ions in a crystal or a solution of a biological macromolecule.

Online 3 February 2009


computer programs


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J. Appl. Cryst. (2009). 42, 336-338  [ doi:10.1107/S0021889808043847 ]

CSSP (Consensus Secondary Structure Prediction): a web-based server for structural biologists

A. Gupta, A. Deshpande, J. K. Amburi, R. Sabarinathan, R. Senthilkumar and K. Sekar

Synopsis: A web-based computing server for consensus prediction of secondary structure was developed. It is available on the World Wide Web at http://bioserver1.physics.iisc.ernet.in/cssp/.

Online 24 January 2009


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J. Appl. Cryst. (2009). 42, 339-341  [ doi:10.1107/S0021889808042726 ]

OLEX2: a complete structure solution, refinement and analysis program

O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann

Synopsis: The program OLEX2 provides tools for the determination, visualization and analysis of molecular crystal structures.

Online 24 January 2009


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J. Appl. Cryst. (2009). 42, 342-346  [ doi:10.1107/S0021889809000338 ]

DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering

D. Franke and D. I. Svergun

Synopsis: DAMMIF, an enhanced and significantly faster implementation of the ab-initio shape-determination program DAMMIN for small-angle scattering data, is presented.

Online 24 January 2009


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J. Appl. Cryst. (2009). 42, 347-353  [ doi:10.1107/S0021889809002222 ]

Irena: tool suite for modeling and analysis of small-angle scattering

J. Ilavsky and P. R. Jemian

Synopsis: Irena, a tool suite of scientific software for analysis of small-angle scattering data, is presented. Models, the graphical user interface and user support tools included in the package as well as software distribution are described.

Online 3 February 2009


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J. Appl. Cryst. (2009). 42, 354-355  [ doi:10.1107/S0021889809002271 ]

Instrumental drift correction by nonparametric statistics

A. Dudka

Synopsis: Instrumental drift correction by nonparametric statistics is described.

Online 7 February 2009


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J. Appl. Cryst. (2009). 42, 356-359  [ doi:10.1107/S0021889809006840 ]

GDASH: a grid-enabled program for structure solution from powder diffraction data

T. A. N. Griffin, K. Shankland, J. van de Streek and J. Cole

Synopsis: A program that exploits a commodity grid to accelerate crystal structure solution from powder diffraction data, using the DASH program, is described.

Online 5 March 2009


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J. Appl. Cryst. (2009). 42, 360-361  [ doi:10.1107/S0021889809006852 ]

MDASH: a multi-core-enabled program for structure solution from powder diffraction data

T. A. N. Griffin, K. Shankland, J. van de Streek and J. Cole

Synopsis: A program that exploits the increasing availability of computers with more than one CPU or with CPUs with multiple cores to accelerate structure solution from powder diffraction data, using the DASH program, is described.

Online 5 March 2009


letters to the editor


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J. Appl. Cryst. (2009). 42, 362-364  [ doi:10.1107/S0021889808044142 ]

Constraints and restraints in crystal structure analysis

A. Immirzi

Synopsis: The restraint-based procedure in least-squares refinement is critiqued and the advantages of using internal coordinates are discussed.

Online 7 February 2009


notes and news


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J. Appl. Cryst. (2009). 42, 365  [ doi:10.1107/S0021889809002775 ]

Lecture demonstrations in a public lecture on `X-ray crystal structure analysis: from W. L. Bragg to the present day'

J. R. Helliwell

Online 3 February 2009


 

J. Appl. Cryst. (2009). 42, 366-368

forthcoming meetings and short courses


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