Journal of Applied Crystallography

Volume 37, Part 4 (August 2004)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Volumetric visualization of electron density surrounding a histidine residue, allowing for direct observation of discrete disorder; generated with POVScript+ and rendered with POVRay. Courtesy of T. D. Fenn, D. Ringe & G. A. Petsko [J. Appl. Cryst. (2003), 36, 944-947].

research papers


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J. Appl. Cryst. (2004). 37, 513-522  [ doi:10.1107/S0021889804010660 ]

X-ray absorption by macromolecular crystals: the effects of wavelength and crystal composition on absorbed dose

J. W. Murray, E. F. Garman and R. B. G. Ravelli

Synopsis: The total radiation dose that can be absorbed by a crystal before the diffraction pattern is destroyed is finite. A program, RADDOSE, is presented that calculates the irradiation time by which the theoretical dose limit is reached for a given crystal and X-ray energy.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 523-535  [ doi:10.1107/S0021889804008969 ]

Particle size distributions from small-angle scattering using global scattering functions

G. Beaucage, H. K. Kammler and S. E. Pratsinis

Synopsis: A detailed consideration of particle size distributions in nanostructured powders determined by small-angle scattering is presented including a direct measure of the width of the particle size distribution and the moments of the distribution for spherical particles. Comparison is made with TEM and gas adsorption data from crystalline pyrolytic powders, as well as with the available techniques for the determination of particle size distribution in scattering.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 536-544  [ doi:10.1107/S0021889804008957 ]

Reverse Monte Carlo with geometric analysis - RMC+GA

S. Wells, M. Dove and M. Tucker

Synopsis: An analysis of simulated framework structure, based on the rigid-unit model and providing a novel way of extracting information from reverse Monte Carlo simulations, is developed. A program called GASP has been developed to perform this analysis and this program is freely available to researchers.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 545-550  [ doi:10.1107/S0021889804009847 ]

CRYSTALS enhancements: refinement of atoms continuously disordered along a line, on a ring or on the surface of a sphere

L. Schröder, D. J. Watkin, A. Cousson, R. I. Cooper and W. Paulus

Synopsis: In cases where there is massive librational disorder, smearing the atomic density out over a simple geometric shape provides a more realistic approximation to the true electron density than using a model consisting of multiply disordered partial atoms. This implementation enables simple geometric shapes to coexist with localized atoms.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 551-554  [ doi:10.1107/S0021889804008921 ]

Birefringence of lead titanate (PbTiO3)

D. Zekria, A. M. Glazer, V. Shuvaeva, J. Dec and S. Miga

Synopsis: This paper reports unexpected results obtained from independent measurements of a selection of recently grown lead titanate crystals, in which the birefringence is some four times greater than hitherto believed. This has important consequences for the use of birefringence measurements as a means of studying phase transitions in crystals.

Online 17 July 2004


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[HTML version][PDF version][Supplementary Material]  [Open access]

J. Appl. Cryst. (2004). 37, 555-564  [ doi:10.1107/S0021889804010052 ]

The role of wavelength and source in the search for sulfur-atom positions evaluated in two case studies: lysozyme at room temperature and cryo apocrustacyanin A1

M. Cianci, J. R. Helliwell, D. Moorcroft, A. Olczak, J. Raftery and P. J. Rizkallah

Synopsis: Lysozyme has been used for an investigation into locating the sulfur anomalous scatterers using rotating anode or synchrotron radiation data recorded at room temperature, thus spanning wavelengths from 0.71 to 2 Å. It was possible to locate the sulfur atoms from a lysozyme crystal at room temperature using softer synchrotron X-rays, the experience thus gained benefiting the case of apocrustacyanin A1.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 565-574  [ doi:10.1107/S0021889804011094 ]

A `beam-selection' high-resolution X-ray diffractometer

P. F. Fewster

Synopsis: A new high-resolution low-noise X-ray diffractometer that requires minimal sample alignment is described. Examples include the analysis of semiconductors in microdiffraction mode, and the study of bent and imperfect samples, and the results are compared with those obtained with other diffractometers.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 575-584  [ doi:10.1107/S0021889804011288 ]

SAXS of self-assembled oriented lamellar nanocomposite films: an advanced method of evaluation

W. Ruland and B. Smarsly

Synopsis: Oriented lamellar nanocomposites formed of alternating organic and inorganic layers were prepared by evaporation-induced self-assembly and studied by small-angle X-ray scattering in symmetrical and asymmetrical reflection. A quantitative fit of the experimental data leads to a comprehensive characterization of the lamellar two-phase system in terms of the average thicknesses of the lamellae, the average period and the corresponding variances, using both the stacking model and the lattice model.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 585-588  [ doi:10.1107/S0021889804011501 ]

X-ray interferometric method for investigation of deformation fields caused in interferometer blocks by implanted ions

H. R. Drmeyan

Synopsis: Lateral deformations caused by argon ions with energy 180 keV implanted in silicon are investigated by the X-ray interferometric method. By means of interferometric topograms, relative deformations and integral stresses are determined depending on radiation dose.

Online 17 July 2004


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

J. Appl. Cryst. (2004). 37, 589-595  [ doi:10.1107/S0021889804011720 ]

The deformation tensor [epsilon] of the spin transition in the mixed crystal [Fe0.46Zn0.54(ptz)6](BF4)2

J. Kusz, H. Spiering and P. Gütlich

Synopsis: Elastic interaction between molecules becomes visible by the change of bond length with the concentration x in an FexZn1-x mixed crystal.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 596-606  [ doi:10.1107/S0021889804012737 ]

Depth capabilities of neutron and synchrotron diffraction strain measurement instruments. I. The maximum feasible path length

P. J. Withers

Synopsis: This paper describes a new approach for estimating the depth capabilities of neutron and synchrotron diffraction instruments for strain measurement. The following paper (part II) uses the framework developed here to evaluate the conditions under which neutron and synchrotron instruments can provide acceptable strain measurements, and delineates the conditions under which the two types of instruments are most suited.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 607-612  [ doi:10.1107/S0021889804012750 ]

Depth capabilities of neutron and synchrotron diffraction strain measurement instruments. II. Practical implications

P. J. Withers

Synopsis: The companion paper (part I) described an approach for calculating the practical penetration length capability of neutron and synchrotron diffraction instruments for strain measurement. The present paper (part II) uses the framework developed in part I to evaluate the conditions under which neutron and synchrotron instruments can provide acceptable strain measurements, and delineates the conditions over which each is most suited.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 613-620  [ doi:10.1107/S0021889804012701 ]

Interference phenomena observed by X-ray diffraction in nanocrystalline thin films

D. Rafaja, V. Klemm, G. Schreiber, M. Knapp and R. Kuzel

Synopsis: A microstructure model for the description of scattering phenomena in nanocrystalline materials is proposed and verified experimentally by a combination of X-ray diffraction and transmission electron microscopy with high resolution. It is shown that nanocrystalline domains can be partially coherent to X-rays at low diffraction angles; the microstructure parameters governing the coherence are the size and the preferred orientation of crystallites.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 621-628  [ doi:10.1107/S0021889804013184 ]

On the equivalence of the Rietveld method and the correlated integrated intensities method in powder diffraction

W. I. F. David

Synopsis: Mathematical aspects of the close relationship between the Rietveld method and the two-stage Pawley and correlated integrated intensities refinement of powder diffraction data are discussed.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 629-634  [ doi:10.1107/S0021889804013366 ]

Nanocrystalline domain size distributions from powder diffraction data

M. Leoni and P. Scardi

Synopsis: The whole-powder-pattern modelling procedure is modified to allow a fast refinement of the grain size distribution for a given crystallite shape, without using any a priori chosen analytical expression. The proposed algorithm is tested both on simulated and on real data for nanocrystalline ceria.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 635-642  [ doi:10.1107/S0021889804013743 ]

High-throughput powder diffraction. III. The application of full-profile pattern matching and multivariate statistical analysis to round-robin-type data sets

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

Synopsis: Multivariate statistical methods are used to analyse a set of 27 powder diffraction patterns of alumina collected at different laboratories on different instruments using the PolySNAP software.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 643-651  [ doi:10.1107/S0021889804013196 ]

Modified Porod's law estimate of the transition-layer thickness between two phases: test of triangular smoothing function

M.-H. Kim

Synopsis: A triangular smoothing function is used to approximate the scattering length density (or electron density) gradient between two phases and an analytical expression to determine the transition-layer thickness is described using the modified Porod law.

Online 17 July 2004


short communications


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J. Appl. Cryst. (2004). 37, 652-653  [ doi:10.1107/S002188980401060X ]

Structural studies of light-induced excited states

A. L. Thompson, A. Beeby and A. E. Goeta

Synopsis: Until now the study of structures under irradiation has been carried out with a `point and fire' approach. This paper presents a device that simplifies laser alignment and makes possible the collection of a full sphere of data without risking obstruction of the incident or scattered X-rays, or the laser beam.

Online 17 July 2004


computer programs


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J. Appl. Cryst. (2004). 37, 654-657  [ doi:10.1107/S0021889804009859 ]

MolViewX: a molecular visualization program for the Macintosh OS X system

T. J. Smith

Synopsis: MolViewX is a molecular visualization tool written for the Macintosh OS X operating system with a graphical user interface designed for occasional or novice users, but which can also be used to create high-quality images rapidly for publication.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 658-664  [ doi:10.1107/S0021889804011173 ]

PolySNAP: a computer program for analysing high-throughput powder diffraction data

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

Synopsis: PolySNAP is a computer program for the analysis of powder diffraction patterns produced in a high-throughput environment. A correlation matrix is generated by matching full-profile powder patterns; this is used by cluster analysis, multivariate data analysis and data visualization routines to classify the patterns automatically into groups and thus identify polymorphs, mixtures and salts.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 665-668  [ doi:10.1107/S0021889804011847 ]

SNAP-1D: a computer program for qualitative and quantitative powder diffraction pattern analysis using the full pattern profile

G. Barr, C. J. Gilmore and J. Paisley

Synopsis: SNAP-1D is a computer program with a novel approach to the qualitative and quantitative analysis of powder diffraction data using the full measured data points. Both non-parametric statistical tests based on Spearman's correlation coefficient and the Kolmogorov-Smirnov test, and more conventional correlations are used to match patterns, and by the use of singular value decomposition techniques, the method can be extended to the quantitative analysis of mixtures.

Online 17 July 2004


CIF applications


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J. Appl. Cryst. (2004). 37, 669-671  [ doi:10.1107/S0021889804009112 ]

CIF applications. XVI. CIF2CRY: for CIF input into the CRYSTALS program

R. I. Cooper, B. M. Foxman and L. Yang

Synopsis: This paper describes the program CIF2CRY for the conversion of structural CIF data into a CRYSTALS input format.

Online 17 July 2004


laboratory notes


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J. Appl. Cryst. (2004). 37, 672-674  [ doi:10.1107/S0021889804012026 ]

The elimination of the influence of ambient environmental effects on the structure of `inert' polymers

L. G. Rosa, P. A. Jacobson, R. Lemoine and P. A. Dowben

Synopsis: The construction and use of a vacuum chamber suitable for conventional X-ray diffraction has revealed the effects of the ambient environment, including moisture, on the bulk structure of very thin polymer films.

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 675  [ doi:10.1107/S0021889804013330 ]

A laboratory furnace for obtaining crystals

B. Cabric and A. Janicijevic

Synopsis: A design for a modular device installed in a laboratory furnace is presented. The setup allows regulation and simultaneous crystallization tests of several substances, with the purpose of obtaining crystals.

Online 17 July 2004


letters to the editor


 

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J. Appl. Cryst. (2004). 37, 676  [ doi:10.1107/S0021889804013780 ]

Comments on Neutron diffraction studies of collagen in human cancellous bone by Skakle & Aspden (2002)

S. Lees

Synopsis: Comments on Skakle & Aspden [J. Appl. Cryst. (2002), 35, 506-508].

Online 17 July 2004


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J. Appl. Cryst. (2004). 37, 677  [ doi:10.1107/S0021889804014116 ]

Response to Lees' comments on Neutron diffraction studies of collagen in human cancellous bone

R. M. Aspden and J. M. S. Skakle

Synopsis: Response to comments on Skakle & Aspden [J. Appl. Cryst. (2002), 35, 506-508].

Online 17 July 2004


computer program abstracts


 

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J. Appl. Cryst. (2004). 37, 678  [ doi:10.1107/S0021889804011744 ]

PDFgetX2: a GUI-driven program to obtain the pair distribution function from X-ray powder diffraction data

X. Qiu, J. W. Thompson and S. J. L. Billinge

Synopsis: PDFgetX2, a GUI-driven program to obtain the pair distribution function from X-ray powder diffraction data, is described.

Online 17 July 2004


 

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J. Appl. Cryst. (2004). 37, 679  [ doi:10.1107/S0021889804015456 ]

Balls&Sticks: easy-to-use structure visualization and animation program

T. C. Ozawa and S. J. Kang

Synopsis: A user-friendly Microsoft Windows-based structure visualization and animation program is presented.

Online 17 July 2004


 

J. Appl. Cryst. (2004). 37, 680-682

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