Journal of Applied Crystallography

Volume 43, Part 4 (August 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


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J. Appl. Cryst. (2010). 43, 665-668  [ doi:10.1107/S0021889810018601 ]

Using the t-distribution to improve the absolute structure assignment with likelihood calculations

R. W. W. Hooft, L. H. Straver and A. L. Spek

Synopsis: This paper describes use of the Student t-distribution to extend the applicability of likelihood methods for absolute structure assignment.

Online 19 June 2010


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J. Appl. Cryst. (2010). 43, 669-676  [ doi:10.1107/S0021889810015608 ]

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart and P. D. Adams

Synopsis: Application of phenix.model_vs_data to the contents of the Protein Data Bank shows that the vast majority of deposited structures can be automatically analyzed to reproduce the reported quality statistics. However, the small fraction of structures that elude automated re-analysis highlight areas where new software developments can help retain valuable information for future analysis.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 677-685  [ doi:10.1107/S0021889810012653 ]

Pattern analysis and interpretation of scattering from short-range order stacking in the layered composite crystal 2H-NaxCoO2·yD2O (x [asymptotically equal to] 0.35, y [asymptotically equal to] 1.3)

M. Onoda, K. Takada and T. Sasaki

Synopsis: The intensity distributions of the Bragg reflections and streaks from 2H-NaxCoO2·yD2O (x [asymptotically equal to] 0.35, y [asymptotically equal to] 1.3) in reciprocal space and their contributions to the powder diffraction pattern are calculated for each HK[zeta], based on the short-range order stacking model using the matrix method, and illustrated.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 686-692  [ doi:10.1107/S0021889810022156 ]

Experimental determination of resolution function parameters from small-angle neutron scattering data of a colloidal SiO2 dispersion

T. Vad, W. F. C. Sager, J. Zhang, J. Buitenhuis and A. Radulescu

Synopsis: The resolution function parameters (geometric contributions as well as wavelength spreads) for the KWS-2 instrument at FRM II have been determined from the small-angle neutron scattering curve of a colloidal silica dispersion with known structure parameters.

Online 1 July 2010


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J. Appl. Cryst. (2010). 43, 693-698  [ doi:10.1107/S0021889810021114 ]

Absorption correction for cylindrical and annular specimens and their containers or supports

M. Bowden and M. Ryan

Synopsis: Formulae for calculating incident and diffracted beam path lengths have been used to calculate the absorption correction in a range of cylindrical geometries. The degree to which this correction is altered by absorption in the capillary used to contain cylindrical specimens, or in the core used to support annular specimens, is shown.

Online 1 July 2010


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J. Appl. Cryst. (2010). 43, 699-709  [ doi:10.1107/S0021889810019163 ]

Temperature-induced structure and microstructure evolution of nanostructured Ni0.9Zn0.1O

A. Kremenovic, B. Antic, M. Vucinic-Vasic, P. Colomban, C. Jovalekic, N. Bibic, V. Kahlenberg and M. Leoni

Synopsis: Ni0.9Zn0.1O nanoparticles annealed in the temperature range 773-1223 K have been studied. The application of a cubic space group to describe the magnetic phase and neglect of a trigonal strain produced by magnetic ordering may result in structure and microstructure modelling errors.

Online 1 July 2010


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J. Appl. Cryst. (2010). 43, 710-715  [ doi:10.1107/S0021889810016870 ]

Unidirectional growth of L-cysteine hydrochloride monohydrate: first time observation as nonlinear optical material and its characterization

G. Bhagavannarayana, S. Kumar, M. Shakir, S. K. Kushawaha, K. K. Maurya, R. Malhotra and K. R. Rao

Synopsis: A large and unidirectional single crystal of L-cysteine hydrochloride monohydrate has been grown for the first time by the recently invented Sankaranarayanan-Ramasamy method. This crystal was found to possess good nonlinear optical properties, which, along with other optical and dielectric properties, revealed that the title compound is a good candidate for photonic applications.

Online 19 June 2010


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J. Appl. Cryst. (2010). 43, 716-719  [ doi:10.1107/S0021889810015773 ]

A new Guinier-Porod model

B. Hammouda

Synopsis: A new Guinier-Porod empirical model is introduced to fit small-angle scattering data from spherical and nonspherical objects such as rods or platelets. This model is used to fit small-angle scattering data from a Pluronic solution that sequentially forms unimers, spherical micelles, cylindrical micelles and lamellar micelles on heating.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 720-728  [ doi:10.1107/S002188981001455X ]

Anomalous thermal expansion of cobalt olivine, Co2SiO4, at low temperatures

A. Sazonov, V. Hutanu, M. Meven, G. Heger, T. Hansen and A. Senyshyn

Synopsis: Anomalous thermal expansion of cobalt olivine, Co2SiO4, is studied by means of both neutron powder and single-crystal diffraction at low temperatures.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 729-736  [ doi:10.1107/S0021889810014688 ]

Experimental setup for in situ X-ray SAXS/WAXS/PDF studies of the formation and growth of nanoparticles in near- and supercritical fluids

J. Becker, M. Bremholm, C. Tyrsted, B. Pauw, K. M. Ø. Jensen, J. Eltzholt, M. Christensen and B. B. Iversen

Synopsis: A versatile setup for in situ synchrotron small/wide-angle X-ray scattering (SAXS/WAXS) and pair distribution function (PDF) measurements of supercritical fluid reactions has been developed.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 737-742  [ doi:10.1107/S0021889810014317 ]

Alternative polymer precipitants for protein crystallization

T. Skálová, J. Dusková, J. Hasek, P. Kolenko, A. Stepánková and J. Dohnálek

Synopsis: A set of 16 polymers was tested for protein crystallization and two new polymer-based protein crystallization screens were formulated.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 743-751  [ doi:10.1107/S0021889810016675 ]

Effects of deviatoric stresses in the diamond-anvil pressure cell on single-crystal samples

J. Zhao, R. J. Angel and N. L. Ross

Synopsis: The nonhydrostatic stress states that are developed in the pressure media within diamond-anvil pressure cells have been investigated by single-crystal X-ray diffraction. The results confirm that the stress state is effectively cylindrically symmetrical with the stress parallel to the load axis being greater than the radial stresses.

Online 5 June 2010


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J. Appl. Cryst. (2010). 43, 752-756  [ doi:10.1107/S0021889810017413 ]

Automated seeding for the optimization of crystal quality

S. Khurshid, L. F. Haire and N. E. Chayen

Synopsis: Automated microseeding protocols are presented.

Online 5 June 2010


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J. Appl. Cryst. (2010). 43, 757-761  [ doi:10.1107/S0021889810016730 ]

Hexagonal and cubic TiOF2

S. Shian and K. H. Sandhage

Synopsis: Titanium oxyflouride, TiOF2, synthesized via a metathetic displacement reaction, was found to possess a hexagonal (R{\\overline 3}c) crystal structure at room temperature, unlike previous reports for this material. Upon heating through 333-338 K, the hexagonal TiOF2 transformed into a cubic (Pm{\\overline 3}m) polymorph.

Online 5 June 2010


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J. Appl. Cryst. (2010). 43, 762-768  [ doi:10.1107/S0021889810016146 ]

Macromolecular crystallography at high pressure with pneumatic diamond anvil cells handled by a six-axis robotic arm

E. Girard, R. Fourme, R. Ciurko, J. Joly, F. Bouis, P. Legrand, J. Jacobs, A.-C. Dhaussy, J.-L. Ferrer, M. Mezouar and R. Kahn

Synopsis: A pneumatic diamond anvil cell for high-pressure macromolecular crystallography is described, and data collection is reported with a robotic arm acting as a goniometer.

Online 5 June 2010


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J. Appl. Cryst. (2010). 43, 769-779  [ doi:10.1107/S0021889810018133 ]

Prediction of hexagonal lattice parameters of various apatites by artificial neural networks

U. Kockan and Z. Evis

Synopsis: Hexagonal lattice parameters of various apatite compounds, M10(TO4)6X2, were predicted from their ionic radii by artificial neural networks. Simple mathematical formulas were derived for the prediction of lattice parameters by using average ionic radii as independent variables.

Online 24 June 2010


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J. Appl. Cryst. (2010). 43, 780-789  [ doi:10.1107/S0021889810013488 ]

Structural stability and optical properties of nanocrystalline zirconia

S. Manna, T. Ghoshal, A. K. Deb and S. K. De

Synopsis: The cubic phase of zirconia is stable at room temperature with decreasing crystallite size. High strain, thermal displacement of atoms and oxygen vacancy play important roles in the thermodynamic phase stability of nanocrystalline zirconia.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 790-797  [ doi:10.1107/S0021889810014184 ]

Scattering from generalized Cantor fractals

A. Y. Cherny, E. M. Anitas, A. I. Kuklin, M. Balasoiu and V. A. Osipov

Synopsis: Analytical formulas are obtained for describing small-angle scattering from generalized Cantor fractals, whose dimensions can be varied from zero to three. The influence of polydispersity on the scattering is considered.

Online 5 June 2010


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J. Appl. Cryst. (2010). 43, 798-804  [ doi:10.1107/S0021889810015499 ]

The dual-space resolution bias correction algorithm: applications to powder data

A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni and R. Rizzi

Synopsis: A dual-space resolution bias correction algorithm has been developed to reduce the truncation effects on electron density maps. The new algorithm has been checked on a set of powder patterns.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 805-810  [ doi:10.1107/S0021889810015980 ]

Comparative study of two lead-free piezoceramics using diffraction techniques

L. A. Schmitt, M. Hinterstein, H.-J. Kleebe and H. Fuess

Synopsis: Two distinct lead-free piezoceramics were investigated by X-ray, neutron and electron diffraction. The experiments revealed the coexistence of rhombohedral R3c and tetragonal P4bm phases.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 811-824  [ doi:10.1107/S0021889810019680 ]

The scientific impact of the Cambridge Structural Database: a citation-based study

R. Wong, F. H. Allen and P. Willett

Synopsis: Citations to 46 scientific articles published by authors based at the Cambridge Crystallographic Data Centre and by external users of the Cambridge Structural Database have been retrieved. Analyses by number of citations and their origins in terms of journals, subject areas and geographic regions are reported.

Online 19 June 2010


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J. Appl. Cryst. (2010). 43, 825-836  [ doi:10.1107/S0021889810018285 ]

From a random to the correct structure: the VLD algorithm

M. C. Burla, C. Giacovazzo and G. Polidori

Synopsis: A new phasing method, based on difference electron-density modification techniques, is described for obtaining the correct structure from a random model.

Online 19 June 2010


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J. Appl. Cryst. (2010). 43, 837-849  [ doi:10.1107/S0021889810017061 ]

Analysing the nanoporous structure of aramid fibres

B. R. Pauw, M. E. Vigild, K. Mortensen, J. W. Andreasen and E. A. Klop

Synopsis: A novel two-dimensional small-angle X-ray scattering pattern analysis method is presented which extracts parameters characterizing the radius, length and polydispersity of scatterers in heat-treated and precursor poly(p-phenylene terephtalamide) fibres.

Online 19 June 2010


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J. Appl. Cryst. (2010). 43, 850-857  [ doi:10.1107/S0021889810015736 ]

Form factor of an N-layered helical tape and its application to nanotube formation of hexa-peri-hexabenzocoronene-based molecules

C. V. Teixeira, H. Amenitsch, T. Fukushima, J. P. Hill, W. Jin, T. Aida, M. Hotokka and M. Lindén

Synopsis: The form factor of a helical tape with N layers is presented. The form factor is used to characterize an intermediate stage in the formation of graphitic nanotubes that self-organize in a two-dimensional hexagonal arrangement.

Online 24 June 2010


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J. Appl. Cryst. (2010). 43, 858-866  [ doi:10.1107/S0021889810019187 ]

Continuous flow supercritical water synthesis and crystallographic characterization of anisotropic boehmite nanoparticles

N. Lock, P. Hald, M. Christensen, H. Birkedal and B. B. Iversen

Synopsis: Nanocrystalline boehmite (AlOOH) was synthesized under continuous flow in sub- and supercritical water. The reaction temperature- and pressure-dependent particle size and morphology were studied using powder X-ray diffraction and transmission electron microscopy.

Online 24 June 2010


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J. Appl. Cryst. (2010). 43, 867-875  [ doi:10.1107/S0021889810019412 ]

Quantitative analysis of diffuse X-ray scattering in partially transformed 3C-SiC single crystals

A. Boulle, D. Dompoint, I. Galben-Sandulache and D. Chaussende

Synopsis: The diffuse X-ray scattering from partially transformed 3C-SiC single crystals is quantitatively analyzed. The transformation mechanisms and the transformation levels are unambiguously determined.

Online 19 June 2010


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J. Appl. Cryst. (2010). 43, 876-882  [ doi:10.1107/S0021889810019576 ]

In-house characterization of protein powder

C. G. Hartmann, O. F. Nielsen, K. Ståhl and P. Harris

Synopsis: X-ray powder diffraction on proteins for identification of polymorphs and precipitates can be carried out on in-house equipment. Experimental patterns compare very well with calculated patterns after correction for background, unit-cell parameters, disordered bulk solvent and geometric factors.

Online 19 June 2010


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J. Appl. Cryst. (2010). 43, 883-889  [ doi:10.1107/S0021889810018340 ]

Diamond plates on dome-like particles: preparation, characterization and field emission properties

R. N. Tiwari, W.-C. Chen, J. N. Tiwari, W.-L. Wang and L. Chang

Synopsis: Structural characterization of crystalline diamond plates on dome-like carbon particles has been carried out using X-ray diffraction and transmission electron microscopy. Application of the Scherrer formula to grain-size analysis, and a possible mechanism for the synthesis of diamond plates and their use in field emission, are discussed.

Online 19 June 2010


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J. Appl. Cryst. (2010). 43, 890-899  [ doi:10.1107/S0021889810019989 ]

X-ray measurement of residual stresses and texture development during a rolling sequence of zirconium alloy cladding tubes - influence of plastic anisotropy on mechanical behaviour

D. Gloaguen, J. Fajoui, E. Girard and R. Guillén

Synopsis: Texture and residual stress analysis using X-ray diffraction has been carried out on zirconium alloy cladding tubes after cold pilgering. A quantitative interpretation of the influence of intergranular stresses on the analysed stress development has been performed using a polycrystalline model.

Online 19 June 2010


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J. Appl. Cryst. (2010). 43, 900-906  [ doi:10.1107/S0021889810021072 ]

Remarkable precision of the 90-year-old dynamic diffraction theories of Darwin and Ewald

M. Agamalian, J. M. Carpenter and W. Treimer

Synopsis: The Bonse-Hart reflectivity functions for a multi-bounce crystal exhibit nearly rectangular profiles, which are different from the experimental results. The results presented here lead to nearly theoretical Bonse-Hart reflectivity profiles and improved sensitivity for the next generation of double-crystal diffractometers.

Online 24 June 2010


short communications


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J. Appl. Cryst. (2010). 43, 907-912  [ doi:10.1107/S0021889810020157 ]

The use of orthogonal projection to visualize mosaic domains from topographic data collected on protein crystals

J. J. Lovelace and G. E. O. Borgstahl

Synopsis: An improved automated approach to extraction of individual mosaic domains from a sequence of topographic images is presented. The only user input is the number of domains that are to be searched for.

Online 24 June 2010


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J. Appl. Cryst. (2010). 43, 913-915  [ doi:10.1107/S0021889810022260 ]

A refinement strategy for Monte Carlo modelling of diffuse scattering from molecular crystal systems

E. J. Chan, T. R. Welberry, D. J. Goossens and A. P. Heerdegen

Synopsis: A new strategy for modelling diffuse scattering from molecular crystals using Monte Carlo simulation is described. Use is made of a simple empirical formula to specify spring constants and provide an objective means for limiting the number of springs needed.

Online 1 July 2010


CIF applications


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J. Appl. Cryst. (2010). 43, 916-919  [ doi:10.1107/S0021889810018145 ]

ASTAR: a .NET class library for STAR/CIF manipulation

Y. Lin

Synopsis: A .NET class library for STAR/CIF manipulation, ASTAR, has been developed.

Online 5 June 2010


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J. Appl. Cryst. (2010). 43, 920-925  [ doi:10.1107/S0021889810022120 ]

publCIF: software for editing, validating and formatting crystallographic information files

S. P. Westrip

Synopsis: The application publCIF is described, with emphasis on its usefulness in validating the syntax and contents of CIFs, and in managing other resources useful for the publication of CIF-based articles.

Online 24 June 2010


computer programs


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J. Appl. Cryst. (2010). 43, 926-928  [ doi:10.1107/S0021889810015013 ]

LauePt, a graphical-user-interface program for simulating and analyzing white-beam X-ray diffraction Laue patterns

X. R. Huang

Synopsis: LauePt is a robust and extremely easy-to-use Windows application for accurately simulating, indexing and analyzing white-beam X-ray diffraction Laue patterns of any crystals under arbitrary diffraction geometry.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 929-936  [ doi:10.1107/S0021889810020352 ]

FitGISAXS: software package for modelling and analysis of GISAXS data using IGOR Pro

D. Babonneau

Synopsis: A software package for performing modelling and analysis of GISAXS data within the distorted wave Born approximation has been developed using the IGOR Pro scripting language.

Online 1 July 2010


laboratory notes


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J. Appl. Cryst. (2010). 43, 937-939  [ doi:10.1107/S0021889810015967 ]

Growth of large protein crystals by a large-scale hanging-drop method

K. Kakinouchi, T. Nakamura, T. Tamada, H. Adachi, S. Sugiyama, M. Maruyama, Y. Takahashi, K. Takano, S. Murakami, T. Inoue, R. Kuroki, Y. Mori and H. Matsumura

Synopsis: A method is described for growing large crystals of proteins; a cut pipette tip is used to hang large-scale droplets (maximum volume 200 µl), enabling the effective manipulation of crystals and the removal of spontaneously nucleated crystals. Large-volume crystals so obtained diffracted neutrons to beyond 3.5 Å resolution.

Online 22 May 2010


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J. Appl. Cryst. (2010). 43, 940-944  [ doi:10.1107/S0021889810018595 ]

Autolabo: an automated system for ligand-soaking experiments with protein crystals

M. Sugahara, K. Shimizu, Y. Asada, H. Fukunishi, H. Kodera, T. Fujii, E. Osada, T. Kasazaki, T. Sawada, H. Chikusa, K. Kondo, A. Yorihiro and N. Kunishima

Synopsis: A new automated system for the ligand soaking of protein crystals has been developed.

Online 19 June 2010


crystallographers


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J. Appl. Cryst. (2010). 43, 945  [ doi:10.1107/S0021889810021424 ]

Gerard Rieck (1911-2010)

Online 24 June 2010


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J. Appl. Cryst. (2010). 43, 946  [ doi:10.1107/S0021889810024246 ]

Lodovico Riva Di Sanseverino (1939-2010)

Online 1 July 2010


book reviews


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J. Appl. Cryst. (2010). 43, 947  [ doi:10.1107/S0021889810014548 ]

Introduction to texture analysis: macrotexture, microtexture and orientation mapping

Online 22 May 2010


 

J. Appl. Cryst. (2010). 43, 948

forthcoming meetings and short courses


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