Journal of Applied Crystallography

 

J. Appl. Cryst. (2008). 41, 1-7  [ doi:10.1107/S0021889807048820 ]

Pressure-induced high-density amorphous ice in protein crystals

C. U. Kim, Y.-F. Chen, M. W. Tate and S. M. Gruner

Synopsis: High-density amorphous ice is shown to occur in high-pressure cryocooled protein crystallization solution and protein crystals, supporting a proposed mechanism for high-pressure cryocooling effects.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 8-17  [ doi:10.1107/S0021889807049308 ]

Automated classification of crystallization experiments using wavelets and statistical texture characterization techniques

D. Watts, K. Cowtan and J. Wilson

Synopsis: The statistical distribution of wavelet coefficient values in each sub-band image is used to provide variables for the classification of images from protein crystallization experiments.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 18-26  [ doi:10.1107/S0021889807049886 ]

Crystal truncation rod X-ray scattering: exact dynamical calculation

V. Holý and P. F. Fewster

Synopsis: A method is developed for an exact calculation of the intensity of X-ray diffraction along a crystal truncation rod.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 27-30  [ doi:10.1107/S0021889807049655 ]

X-ray scattering study of the average polycyclic aromatic unit in Ledo coal

R. K. Boruah, B. K. Saikia, B. P. Baruah and N. C. Dey

Synopsis: Through an X-ray scattering analysis, the short-range structural features, the relationship(s) between the aryl/alkyl carbon ratio, and the size of the average polycyclic aromatic unit in Ledo coal from Makum coalfield, Assam, India, are elucidated.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 31-37  [ doi:10.1107/S0021889807049898 ]

Phase perturbation as a means of electron density map quality evaluation

O. Kirillova

Synopsis: A new way for evaluating the quality of crystallographic electron density maps is described. It has been found that a high-quality map possesses greater robustness against perturbations applied to the phases.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 38-43  [ doi:10.1107/S0021889807050029 ]

Gasketing optimized for large sample volume in the diamond anvil cell: first application to MgGeO₃ and implications for structural systematics of the perovskite to post-perovskite transition

C. D. Martin, Y. Meng, V. Prakapenka and J. B. Parise

Synopsis: Improved post-perovskite structure models of MgGeO₃ (Cmcm) are obtained via development of a new graphite gasket for the diamond anvil cell which increases the volume of sample and quality of diffraction data at pressures near 100 GPa. These models agree with a structure survey supporting a new method for estimating the Clapeyron slope between perovskite (Pbnm) and post-perovskite structures of MgSiO₃.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 44-55  [ doi:10.1107/S0021889807051175 ]

Unified description for the geometry of X-ray stress analysis: proposal for a consistent approach

M. François

Synopsis: A consistent scheme for describing the geometry of X-ray stress acquisition is proposed. It allows derivation of all the classical acquisition modes described in the literature by distinguishing angles related to the physics of diffraction, angles related to the goniometer and angles probing the specimen.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 56-61  [ doi:10.1107/S0021889807054192 ]

Direct methods and simulated annealing: a hybrid approach for powder diffraction data

A. Altomare, R. Caliandro, C. Cuocci, C. Giacovazzo, A. G. G. Moliterni, R. Rizzi and C. Platteau

Synopsis: The procedure implemented in a previous version of EXPO combining a Monte Carlo approach with the information contained in the Fourier map as obtained at the end of a direct-methods procedure has been revised and improved.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 62-67  [ doi:10.1107/S0021889807054398 ]

Phased rotation, conformation and translation function: performance with mononucleotides

F. Pavelcik

Synopsis: The phased rotation, conformation and translation function was applied to nucleic acid structures; the search fragment is a mononucleotide extended by a phosphate group. 50 to 93% of fragments can be located depending on the resolution and phase quality.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 68-82  [ doi:10.1107/S0021889807054453 ]

Theoretical investigation of (MgCl₂)_x polynuclear species formed during preparation of MgCl₂-supported Ziegler-Natta catalysts from solid solvates

F. Auriemma and C. De Rosa

Synopsis: Models of (MgCl₂)_x polynuclear structures are built and a method for the calculation of the X-ray powder diffraction patterns of the models is devised. The calculated diffraction patterns of these model structures may be useful to interpret the structural evolution of solid solvates of MgCl₂ with Lewis bases during the preparation of the heterogeneous catalyst systems used for Ziegler-Natta polymerization of olefins.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 83-95  [ doi:10.1107/S002188980705621X ]

Determination of site occupancies by the intermeasurement minimization method. I. Anomalous scattering usage for noncentrosymmetric crystals

A. Dudka

Synopsis: New methods for determination of the site occupancy factors in noncentrosymmetric crystals using reductions of the anomalous scattering contribution and the intermeasurement minimization method are described

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 96-103  [ doi:10.1107/S0021889807059870 ]

Determination of absolute structure using Bayesian statistics on Bijvoet differences

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

Synopsis: A description is given of a maximum-likelihood approach to absolute structure determinations of biologically active molecules.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 104-109  [ doi:10.1107/S0021889807065235 ]

Metalloproteins: metal binding predicted on the basis of the amino acid sequence

O. Carugo

Synopsis: Uptake of metal ions by proteins can be predicted on the basis of the amino acid composition, by using a mixture of several simplified amino acid alphabets and by employing machine learning methods, with 70-90% accuracy, depending on the type of metal.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 110-114  [ doi:10.1107/S0021889807048765 ]

Accessible reciprocal-space region for non-coplanar Bragg and Laue geometries

O. Yefanov

Synopsis: The correct three-dimensional shape of the accessible reciprocal-space region for a given plane of incidence is plotted and formulae for finding the experimental geometry for any reciprocal node are given.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 115-123  [ doi:10.1107/S002188980704976X ]

Using the general equation of a conic for the calculation of the instrument function of a Bragg-Brentano diffractometer

A. D. Zuev

Synopsis: Simple equations of the diffraction and reflection conics as second degree polynomials in the receiving-slit plane of a Bragg-Brentano diffractometer are given and applied to the analysis of the instrument functions.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 124-133  [ doi:10.1107/S0021889807050005 ]

Application of a single-reflection collimating multilayer optic for X-ray diffraction experiments employing parallel-beam geometry

M. Wohlschlögel, T. U. Schülli, B. Lantz and U. Welzel

Synopsis: The performance of a diffractometer equipped with a rotating anode source, a single-reflection collimating multilayer optic which can collimate an X-ray beam in two mutually perpendicular planes and a parallel-plate collimator in front of the detector has been characterized in detail. Its capabilities have been illustrated by ray-tracing calculations for the multilayer optic and by standard powder diffraction experiments.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 134-142  [ doi:10.1107/S0021889807051345 ]

Structural characterization using the multiple scattering effects in grazing-incidence small-angle X-ray scattering

B. Lee, C.-T. Lo, P. Thiyagarajan, D. R. Lee, Z. Niu and Q. Wang

Synopsis: The multiple scattering effects present in grazing-incidence small-angle X-ray scattering (GISAXS) data and interference between them are addressed theoretically as well as experimentally with measurement of a series of patterns at different incident angles, referred to as `incident-angle-resolved GISAXS' (IAR-GISAXS). X-ray reflectivity, GISAXS and IAR-GISAXS of virus particles on Si-substrate supported-polystyrene films have been measured and all the data have been analyzed with appropriate formalisms.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 143-152  [ doi:10.1107/S0021889807051904 ]

Reproducibility in X-ray reflectometry: results from the first world-wide round-robin experiment

P. Colombi, D. K. Agnihotri, V. E. Asadchikov, E. Bontempi, D. K. Bowen, C. H. Chang, L. E. Depero, M. Farnworth, T. Fujimoto, A. Gibaud, M. Jergel, M. Krumrey, T. A. Lafford, A. Lamperti, T. Ma, R. J. Matyi, M. Meduna, S. Milita, K. Sakurai, L. Shabel'nikov, A. Ulyanenkov, A. Van der Lee and C. Wiemer

Synopsis: Results of the first world-wide round-robin experiment on X-ray reflectometry (XRR) are presented and discussed. The investigation aims to assess the reproducibility of XRR measurements and analysis, and to produce a `good practice' manual for this technique.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 153-160  [ doi:10.1107/S0021889807055069 ]

Application of the X-ray tracing method to powder diffraction line profiles

S. Lambert and F. Guillet

Synopsis: An X-ray tracing program was developed to simulate the instrument function of a laboratory high-resolution X-ray powder diffractometer. The results provide the basis for discussing the opportunity of using X-ray tracing in diagram-refinement software.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 161-166  [ doi:10.1107/S0021889807056361 ]

Toward a new lower limit for the minimum scattering vector on the very small angle neutron scattering spectrometer at Laboratoire Léon Brillouin

A. Brûlet, V. Thévenot, D. Lairez, S. Lecommandoux, W. Agut, S. P. Armes, J. Du and S. Désert

Synopsis: High-resolution neutron scattering data down to q = 4 × 10^-3 nm^-1 can be obtained using the very small angle neutron scattering spectrometer under construction at the Laboratoire Léon Brillouin. While still under construction, the new instrument has successfully allowed completion of the scattering curve of vesicles of 500 nm radii toward the smaller scattering vector range.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 167-175  [ doi:10.1107/S0021889807056944 ]

High hydrostatic pressure small-angle X-ray scattering cell for protein solution studies featuring diamond windows and disposable sample cells

N. Ando, P. Chenevier, M. Novak, M. W. Tate and S. M. Gruner

Synopsis: A user-friendly high-pressure cell for synchrotron small-angle X-ray scattering studies of protein solutions is described. Disposable inner sample cells facilitate sample isolation, minimization and handling.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 176-184  [ doi:10.1107/S0021889807057822 ]

Web-Ice: integrated data collection and analysis for macromolecular crystallography

A. González, P. Moorhead, S. E. McPhillips, J. Song, K. Sharp, J. R. Taylor, P. D. Adams, N. K. Sauter and S. M. Soltis

Synopsis: Web-Ice is a scalable, extendable and portable software application for rapid on-line diffraction image analysis, autoindexing and strategy calculation. The Web-Ice architecture, software components and functionality, both as a stand-alone application and as part of a beamline control system, are described.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 185-190  [ doi:10.1107/S0021889807058074 ]

Two-dimensional focusing of high-energy X-rays by thermal-gradient crystals for small-angle X-ray scattering

M. Stockmeier, M. Petermair and A. Magerl

Synopsis: A novel method for focusing X-rays in two dimensions by thermal-gradient crystals in symmetrical Laue geometry is described. The intensity in the focal point can be increased significantly by using thermal-gradient crystals.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 191-197  [ doi:10.1107/S0021889807064011 ]

A simple method for analyzing peak broadening due to tilt and twist distributions in X-ray diffraction measurements of materials of arbitrary type

K. Nakashima and T. Matsuoka

Synopsis: A new method for simply identifying the X-ray diffraction peak broadening caused by tilt and twist distributions through analysis of their hkl dependence is proposed. The method for twist distributions is experimentally demonstrated using GaN epitaxial films on sapphire substrates.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 198-205  [ doi:10.1107/S0021889807065806 ]

Flat-plate single-crystal silicon sample holders for neutron powder diffraction studies of highly absorbing gadolinium compounds

D. H. Ryan and L. M. D. Cranswick

Synopsis: A flat-plate single-crystal sample holder is used to place a thin layer of highly absorbing samarium and gadolinium compounds in a neutron beam and obtain Rietveld refinement quality diffraction data in a modest time. Demonstration data are presented on two intermetallic compounds, Sm₃Ag₄Sn₄ and Gd₃Ag₄Sn₄, and it is shown that both structural and magnetic information can be derived from the diffraction patterns.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 206-209  [ doi:10.1107/S0021889807060803 ]

Enclosed chambers for humidity control and sample containment in fiber diffraction

M. McDonald, A. Kendall, M. Tanaka, J. S. Weissman and G. Stubbs

Synopsis: Compact, inexpensive, easily constructed sample holders for fiber diffraction allow humidity control, stretching and exposure to magnetic fields during fiber preparation, and primary containment for toxic and infectious biological materials.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 210-213  [ doi:10.1107/S0021889807055458 ]

Imposed stress and variant selection: the role of symmetry and initial texture

P. S. Bate and W. B. Hutchinson

Synopsis: The paper discusses the role of stress on displacive phase transformations where plasticity is associated with variant selection, together with its implications for the resulting texture.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 214-216  [ doi:10.1107/S0021889807057251 ]

A simple and inexpensive capillary furnace for variable-temperature X-ray diffraction

C. Lavigueur, E. J. Foster and V. E. Williams

Synopsis: A small, simple and inexpensive capillary furnace has been developed for variable-temperature X-ray diffraction of liquid crystals and other organic materials.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 217-218  [ doi:10.1107/S0021889807050054 ]

mtz2sca and mtz2hkl: facilitated transition from CCP4 to the SHELX program suite

T. Grune

Synopsis: Two programs are presented that facilitate the transition to refining macromolecular data with the SHELX suite. mtz2sca is used to convert data processed and integrated with MOSFLM into sca format for further processing with SHELXC and SHELXD; mtz2hkl is used to convert an mtz file used for refinement in REFMAC5 into or format for refinement with SHELXL or SHELXH.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 219-221  [ doi:10.1107/S0021889807053708 ]

RPMS: Ramachandran plot for multiple structures

K. Gopalakrishnan, S. Saravanan, R. Sarani and K. Sekar

Synopsis: The web-based interactive computing server RPMS was developed to visualize the conformational angles ( and ) of multiple highly homologous protein structures in a single Ramachandran plot.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 222-226  [ doi:10.1107/S0021889807055136 ]

MULCh: modules for the analysis of small-angle neutron contrast variation data from biomolecular assemblies

A. E. Whitten, S. Cai and J. Trewhella

Synopsis: A description is given of software that allows small-angle neutron contrast variation data of two-component biomolecular assemblies to be analysed in a straightforward manner.

Online 16 January 2008

 

J. Appl. Cryst. (2008). 41, 227-232  [ doi:10.1107/S0021889807060037 ]

Notes for authors 2008

Online 16 January 2008