Journal of Applied Crystallography

Volume 43, Part 1 (February 2010)



[Issue Author Index][Volume Author Index]
[Cover illustration] 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].

research papers


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 1-7  [ doi:10.1107/S0021889809044112 ]

In-situ small-angle neutron scattering study of pore filling and pore emptying in ordered mesoporous silica

M. Erko, D. Wallacher, A. Brandt and O. Paris

Synopsis: The capillary condensation and capillary emptying of water and perfluoropentane in ordered mesoporous SBA-15 silica is studied by in-situ small-angle neutron scattering (SANS). The SANS data can be perfectly described by a simple analytical model for spatially random pore filling (Laue scattering) for the entire range of pore-filling fractions.

Online 1 December 2009


 

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 8-11  [ doi:10.1107/S0021889809048675 ]

Multiphase approximation for small-angle scattering

D. Tatchev

Synopsis: The theory of small-angle scattering of a multiphase system, its relation to scattering contrast variation and the ability to extract the scattering pattern of a single phase are considered.

Online 9 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 12-16  [ doi:10.1107/S0021889809048791 ]

A novel model for the interpretation of small-angle scattering experiments of self-affine structures

G. J. Schneider and D. Göritz

Synopsis: A novel theory is presented which allows the analytical description of small-angle scattering experiments on anisotropic shaped clusters of nanoparticles. Experimentally, silica-filled rubber which is deformed is used as an example.

Online 9 December 2009


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

J. Appl. Cryst. (2010). 43, 17-26  [ doi:10.1107/S002188980904758X ]

Anisotropic microstrain broadening of minium, Pb3O4, in a high-pressure cell: interpretation of line-width parameters in terms of stress variations

A. Leineweber and R. E. Dinnebier

Synopsis: The diffraction-line broadening exhibited by three different Pb3O4 phases was studied at ambient and elevated pressures. The broadening indicates strongly anisotropic microstrain, which was interpreted in terms of (local) stress variations in association with strongly anisotropic elastic properties.

Online 18 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 27-32  [ doi:10.1107/S0021889809051577 ]

Refinement of the [lambda]/2 contribution to CCD detector data

A. Dudka

Synopsis: A new method is proposed to improve structure modeling by taking into account the half-wavelength contribution ([lambda]/2) to X-ray data measured on CCD and image-plate diffractometers.

Online 6 January 2010


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 33-37  [ doi:10.1107/S0021889809050936 ]

Revised phase diagram for the Nd-Pt system from 35 to 85 at% platinum

Ch. F. Xu, Z. F. Gu, G. Cheng, H. Y. Zhou, Z. M. Wang, X. M. Liu, Q. Y. Han and M. H. Jiang

Synopsis: The phase diagram of the Nd-Pt system from 35 to 85 at%Pt has been revised using X-ray diffraction and differential thermal analysis.

Online 6 January 2010


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 38-41  [ doi:10.1107/S0021889809047037 ]

Evidence of extinction in strongly textured high-purity copper

J. Palacios Gomez, J. M. Walter, E. Jansen and T. Kryshtab

Synopsis: Extinction has been found on pole figures measured by neutron diffraction on highly textured high-purity copper. A possible mechanism responsible for the extinction is proposed.

Online 12 January 2010


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 42-47  [ doi:10.1107/S0021889809047748 ]

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

A. Milicevic and N. Raos

Synopsis: This article defines optimal steric crowding around an apical water molecule. The apical bond length shows sigmoidal dependence on distortion of the coordination polyhedron.

Online 9 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 48-52  [ doi:10.1107/S0021889809050547 ]

Drawing of single-crystal and glass-clad lithium tantalate fibers by the laser-heated pedestal growth method

S. C. Pei, T. S. Ho, T. M. Tai, L. M. Lee, J. C. Chen, A. H. Kung, F. J. Kao and S. L. Huang

Synopsis: Lithium tantalate (LT) single-crystalline fibers with various growth conditions were obtained using the laser-heated pedestal growth (LHPG) method. To facilitate wave propagation with low loss, glass-clad LT fibers were fabricated by a co-drawing LHPG method for the first time.

Online 18 December 2009


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

J. Appl. Cryst. (2010). 43, 53-57  [ doi:10.1107/S002188980904134X ]

Automated least-squares molecular overlay without a priori atomic correspondence or connectivity information

A. D. Bond

Synopsis: A method is described for automated least-squares molecular overlay without a priori atomic correspondence or connectivity information. The method is applied to compare crystallographically distinct molecules in 18 941 single-component molecular crystal structures taken from the Cambridge Structural Database.

Online 18 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 58-63  [ doi:10.1107/S0021889809051917 ]

The use of novel organic gels and hydrogels in protein crystallization

Z. Pietras, H.-T. Lin, S. Surade, B. Luisi, O. Slattery, K. M. Pos and A. Moreno

Synopsis: This report describes the application of organic solvent gels and aqueous hydrogels for crystallization of soluble and membrane proteins. The hydrogel is based on polyvinyl alcohol and the organic based gels are formed using polyethylene oxide, which is compatible with a variety of solvents. Diffracting crystals were obtained with both gel systems.

Online 6 January 2010


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 64-69  [ doi:10.1107/S0021889809046342 ]

X-ray absorption fine structure for single crystals

C. T. Chantler, C. Q. Tran and Z. Barnea

Synopsis: This paper describes a technique for collecting X-ray absorption fine structure from perfect crystals, free of large systematic errors.

Online 1 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 70-82  [ doi:10.1107/S0021889809043234 ]

EVAL15: a diffraction data integration method based on ab initio predicted profiles

A. M. M. Schreurs, X. Xian and L. M. J. Kroon-Batenburg

Synopsis: EVAL15, a novel diffraction data integration method, predicts reflection profiles that are used to determine accurate intensities. It can solve a range of difficult diffraction problems, such as those related to overlap, K[alpha]1/K[alpha]2 peak splitting and satellite reflections.

Online 1 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 83-88  [ doi:10.1107/S0021889809046548 ]

Estimation of the centre of a diffraction peak by triggering the goniometer-angle readings via photon detection

G. Mana, J. Krempel and L. Ferroglio

Synopsis: In nuclear spectroscopy by crystal diffraction, Bayesian inference allows [gamma]-ray photons and rocking angles detected in coincidence to be used to find the location of the diffraction peak without binning the recorded angles.

Online 9 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 89-100  [ doi:10.1107/S0021889809050535 ]

Ab initio structure solution by iterative phase-retrieval methods: performance tests on charge flipping and low-density elimination

F. Fleischer, T. Weber, S. Deloudi, L. Palatinus and W. Steurer

Synopsis: The phase-retrieving performance of the structure solution methods charge flipping and low-density elimination is investigated. The best strategies are discussed.

Online 6 January 2010


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

J. Appl. Cryst. (2010). 43, 101-109  [ doi:10.1107/S0021889809043076 ]

Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale

H. Fischer, M. de Oliveira Neto, H. B. Napolitano, I. Polikarpov and A. F. Craievich

Synopsis: A novel procedure for the determination of the molecular weight of proteins in dilute solution from a single small-angle X-ray scattering curve measured on a relative scale is described.

Online 1 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 110-121  [ doi:10.1107/S0021889809043271 ]

A small/wide-angle X-ray scattering instrument for structural characterization of air-liquid interfaces, thin films and bulk specimens

U.-S. Jeng, C. H. Su, C.-J. Su, K.-F. Liao, W.-T. Chuang, Y.-H. Lai, J.-W. Chang, Y.-J. Chen, Y.-S. Huang, M.-T. Lee, K.-L. Yu, J.-M. Lin, D.-G. Liu, C.-F. Chang, C.-Y. Liu, C.-H. Chang and K. S. Liang

Synopsis: A newly installed small/wide-angle X-ray scattering (SAXS/WAXS) instrument for structural characterization is described. The instrument performance is illustrated via a variety of measurements, including simultaneous SAXS/WAXS and grazing-incidence SAXS from the air-water interface.

Online 1 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 122-133  [ doi:10.1107/S0021889809043957 ]

Micropipe-induced birefringence in 6H silicon carbide

T. Ouisse, D. Chaussende and L. Auvray

Synopsis: The micropipe-induced birefringence of 6H silicon carbide is measured and quantitatively modelled, using the rotating polarizer method.

Online 9 December 2009


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

J. Appl. Cryst. (2010). 43, 134-139  [ doi:10.1107/S0021889809045889 ]

Misorientations in rolled and recrystallized zirconium compared with random distribution. A new scheme of misorientation analysis

B. Bacroix, J. Tarasiuk, K. Wierzbanowski and K. Zhu

Synopsis: This work provides a new methodology for the analysis of misorientations in textured materials; its aim is also to shed some light on the development of recrystallization textures in hexagonal materials, which are still largely not understood.

Online 9 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 140-150  [ doi:10.1107/S0021889809049851 ]

An electron diffraction and Monte Carlo simulation study of an incommensurate antiferroelectric state in the relaxor ferroelectric Pb2ScTaO6

K. Z. Baba-Kishi and M. Pasciak

Synopsis: Incommensurate satellite reflections modulating along the <110>* directions have been observed in the electron diffraction patterns of single crystals of the relaxor ferroelectric Pb2ScTaO6 (PST). The satellites represent a weak frustrated antiferroelectric state in PST, termed the incommensurate antiferroelectric state.

Online 18 December 2009


thumbnail of article figure

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

J. Appl. Cryst. (2010). 43, 151-153  [ doi:10.1107/S0021889809048006 ]

X-ray diffraction study of a pseudo single crystal prepared from a crystal belonging to point group 2

F. Kimura, T. Kimura, W. Oshima, M. Maeyama and K. Aburaya

Synopsis: A pseudo single crystal of sucrose (monoclinic, P21) was prepared and the origin of its twin orientation is discussed.

Online 18 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 154-162  [ doi:10.1107/S0021889809050560 ]

Enhancement of SHG efficiency by urea doping in ZTS single crystals and its correlation with crystalline perfection as revealed by Kurtz powder and high-resolution X-ray diffraction methods

G. Bhagavannarayana and S. K. Kushwaha

Synopsis: Urea doping leads to the enhancement of second-harmonic generation (SHG) efficiency in tristhioureazinc(II) sulfate (ZTS) single crystals, with a critical dependence on urea concentration. An interesting correlation between crystalline perfection and SHG efficiency has been revealed using high-resolution X-ray diffractometry and Kurtz powder techniques.

Online 6 January 2010


thumbnail of article figure

[HTML version][PDF version][CIF][3d view]  [Buy article online]

J. Appl. Cryst. (2010). 43, 163-167  [ doi:10.1107/S0021889809047499 ]

Crystal structure study of selected xanthine derivatives

W. Lasocha, B. Gawel, A. Rafalska-Lasocha, M. Pawlowski, P. Talik and W. Paszkowicz

Synopsis: The crystal structures of two pharmaceutical compounds were solved from laboratory and high-resolution powder diffraction data collected at the ESRF Grenoble. The serious problems encountered during an ab initio crystal structure solution from powder data are described and discussed.

Online 12 January 2010


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 168-175  [ doi:10.1107/S0021889809052753 ]

An investigation of the properties of large crystals of the zeolites dodecasil-3C and ferrierite by high-temperature birefringence microscopy and X-ray diffraction

Z. A. D. Lethbridge, D. S. Keeble, D. Walker, P. A. Thomas and R. I. Walton

Synopsis: Large crystals of two siliceous zeolites have been grown and studied as a function of temperature using bifrefringence microscopy. In one case organic template is retained and the crystals show a reversible, ferroelastic phase transition on heating and cooling, but in another the bifrefringence indicates migration of organic template to the crystal edges upon heating.

Online 19 January 2010


short communications


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 176-178  [ doi:10.1107/S0021889809048109 ]

Linearly graded GeSi beam-expanding/compressing X-ray monochromator

D. Korytár, C. Ferrari, P. Mikulík, P. Vagovic, E. Dobrocka, V. Ác, P. Konopka, A. Erko and N. Abrosimov

Synopsis: A V-shaped channel-cut X-ray monochromator based on a graded Ge-rich GeSi single crystal with a total asymmetry factor of 21 is presented. It exhibited a peak intensity more than three times higher than that of a V-21 monochromator made of a pure Ge crystal.

Online 9 December 2009


computer programs


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 179-180  [ doi:10.1107/S0021889809049875 ]

An approach for eliminating chemically unreasonable structure models with overlapping atoms as implemented within the GEST software

Z. J. Feng, R. R. Jia, C. Dong, S. X. Cao and J. C. Zhang

Synopsis: A close-contact penalty factor has been added to the GEST structure solution from powder diffraction data software to differentiate chemically unreasonable structure models from potentially correct models. It has proved an effective method to eliminate chemically unreasonable trial models.

Online 18 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 181-185  [ doi:10.1107/S0021889809051929 ]

ISAACS - interactive structure analysis of amorphous and crystalline systems

S. Le Roux and V. Petkov

Synopsis: A cross-platform program, ISAACS, has been developed to analyze the structural properties of three-dimensional structure models obtained using computer simulations (molecular dynamics, ab-initio molecular dynamics, reverse Monte Carlo, Monte Carlo etc.). A wide range of calculations can be performed, including radial distribution functions, simulation of neutron and X-ray diffraction, ring statistics, and spherical harmonics.

Online 12 January 2010


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

J. Appl. Cryst. (2010). 43, 186-190  [ doi:10.1107/S0021889809045701 ]

xia2: an expert system for macromolecular crystallography data reduction

G. Winter

Synopsis: An expert system for macromolecular crystallography data reduction using existing software, xia2, is presented with examples of its application to a range of data sets.

Online 1 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 191-195  [ doi:10.1107/S0021889809049267 ]

EXTRAX: an ImageJ plug-in for electron diffraction intensity extraction

V. Dorcet, X. Larose, C. Fermin, M. Bissey and P. Boullay

Synopsis: A plug-in (EXTRAX) has been developed for ImageJ - a public domain Java-based program widely used for image processing and analysis in microscopy. This plug-in allows the extraction and measurement of intensities from electron diffraction spot patterns with a semi-automatic peak location based on a two-dimensional lattice given by the user.

Online 18 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 196-199  [ doi:10.1107/S002188980903982X ]

MIPS: metal interactions in protein structures

K. Hemavathi, M. Kalaivani, A. Udayakumar, G. Sowmiya, J. Jeyakanthan and K. Sekar

Synopsis: A web-accessible resource has been created to study the interactions of various metal ions present in macromolecular structures.

Online 1 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 200-202  [ doi:10.1107/S0021889809048626 ]

MLDB: macromolecule ligand database

S. E. Saravanan, R. Karthi, K. Sathish, K. Kokila, R. Sabarinathan and K. Sekar

Synopsis: An online web server coupled with a knowledgebase has been created to study the interactions of various ligand molecules with three-dimensional macromolecular structures.

Online 9 December 2009


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 203-205  [ doi:10.1107/S0021889809047050 ]

SSMBS: a web server to locate sequentially separated motifs in biological sequences

C. Kumar and K. Sekar

Synopsis: This paper describes a computing server, SSMBS, which can locate and display the occurrences of user-defined biologically important sequence motifs (a maximum of five) present in a specific order in protein and nucleotide sequences.

Online 9 December 2009


laboratory notes


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

J. Appl. Cryst. (2010). 43, 206-210  [ doi:10.1107/S0021889809049693 ]

Safety considerations with top-loading cryostats, involving `icing-up' of the sample space with solid air

I. P. Swainson and L. M. D. Cranswick

Synopsis: Safety considerations involving `icing-up' with solid air of the sample space of top-loading cryostat equipment are discussed, where uncontrolled de-icing may cause a flash-to-gas, leading to trapped volumes being placed under high pressure. Methods of prevention and resolution of freeze-ups are elaborated, and a case is made for using a helium leak detector as part of sample changing.

Online 18 December 2009


international union of crystallography


 

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

J. Appl. Cryst. (2010). 43, 211-215  [ doi:10.1107/S0021889809047876 ]

Notes for authors 2010

Online 6 January 2010


 

J. Appl. Cryst. (2010). 43, 216-220

forthcoming meetings and short courses


Copyright © International Union of Crystallography
IUCr Webmaster