Journal of Applied Crystallography

Volume 38, Part 3 (June 2005)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Secondary electron image of a crystalline iron ore sinter phase, produced by heating to 1533 K and then cooling. Courtesy of N. V. Y. Scarlett, I. C. Madsen, M. I. Pownceby & A. N. Christensen [J. Appl. Cryst. (2004), 37, 362-368].

research papers


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J. Appl. Cryst. (2005). 38, 405-411  [ doi:10.1107/S0021889805004875 ]

UB matrix implementation for inelastic neutron scattering experiments

M. D. Lumsden, J. L. Robertson and M. Yethiraj

Synopsis: The UB matrix approach has been extended to inelastic neutron scattering instruments, with calculations presented for triple-axis and time-of-flight spectrometers.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 412-419  [ doi:10.1107/S0021889805005029 ]

Sample size: an important parameter in flash-cooling macromolecular crystallization solutions

U. Chinte, B. Shah, K. DeWitt, K. Kirschbaum, A. A. Pinkerton and C. Schall

Synopsis: Cryoprotectant requirements for successful flash-cooling of protein precipitant solutions were determined; these requirements were found to be a strong function of cryoloop size and appear to correlate with the glass transition temperature of the solution. Detailed key data are presented in tabular form.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 420-425  [ doi:10.1107/S0021889805005157 ]

Structural analysis of single wool fibre by scanning microbeam SAXS

Y. Kajiura, S. Watanabe, T. Itou, A. Iida, Y. Shinohara and Y. Amemiya

Synopsis: The inhomogeneity in the nanostructure of a single wool fibre was investigated by scanning microbeam small-angle X-ray scattering.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 426-432  [ doi:10.1107/S0021889805005637 ]

Correction for counting losses in X-ray diffractometry

T. Ida and Y. Iwata

Synopsis: Models for counting losses in X-ray detection systems are examined. A convenient and versatile formula for correcting count losses is presented.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 433-441  [ doi:10.1107/S0021889805005686 ]

Determining metal ion distributions using resonant scattering at very high-energy K-edges: Bi/Pb in Pb5Bi6Se14

Y. Zhang, A. P. Wilkinson, P. L. Lee, S. D. Shastri, D. Shu, D.-Y. Chung and M. G. Kanatzidis

Synopsis: The distribution of Pb/Bi over the 11 crystallographically distinct sites in Pb5Bi6Se14 was determined from resonant scattering data that had been recorded at ~86 keV, and just below both the Pb and Bi K-edges, using an imaging plate detector and synchrotron radiation.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 442-447  [ doi:10.1107/S0021889805005819 ]

Simulation of threading dislocation images in X-ray topographs of silicon carbide homo-epilayers

W. M. Vetter, H. Tsuchida, I. Kamata and M. Dudley

Synopsis: X-ray topographic images of the threading edge, axial screw and basal plane dislocations that occur in SiC epilayers deposited on offcut SiC substrates are computer simulated and compared with experimental topographs.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 448-454  [ doi:10.1107/S002188980500590X ]

Study of point defects in as-grown and annealed bismuth germanate single crystals

G. Bhagavannarayana, A. Choubey, Yu. V. Shubin and K. Lal

Synopsis: Point defects and their clusters in bismuth germanate single crystals free from grain boundaries and having low density of dislocations were studied by high-resolution diffuse X-ray scattering measurements.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 455-461  [ doi:10.1107/S0021889805006096 ]

A bound constrained conjugate gradient solution method as applied to crystallographic refinement problems

A. A. Coelho

Synopsis: Small modifications to the conjugate gradient method for solving symmetric positive definite systems have resulted in an increase in performance over LU decomposition by a factor of around 84 for solving a dense system of 1325 unknowns. Performance is further increased in the case of applying upper- and lower-bound parameter constraints.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 462-475  [ doi:10.1107/S0021889805006187 ]

Quantitative texture analysis with the HIPPO neutron TOF diffractometer

S. Matthies, J. Pehl, H.-R. Wenk, L. Lutterotti and S. C. Vogel

Synopsis: One of the design goals of the neutron time-of-flight (TOF) diffractometer HIPPO (High Pressure-Preferred Orientation) at LANSCE (Los Alamos Neutron Science Center) was efficient quantitative texture analysis. In this paper, the effects of the HIPPO detector geometry and layout on texture analysis, particularly the shape and dimensions of the detector panels, are investigated in detail.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 476-487  [ doi:10.1107/S0021889805006382 ]

Displacements induced by different nanoprecipitates: a SAXS and WAXS anomalous study on Cu-Ni-Fe and Cu-Ni-Co single crystals

O. Lyon, I. Guillon, C. Servant and J. P. Simon

Synopsis: Single crystals of different Cu-Ni-Co and Cu-Ni-Fe alloys, forming spheroid or plate-like precipitates during decomposition, have been studied by small-angle (SAXS) and wide-angle X-ray scattering (WAXS). The SAXS patterns gave information on the sizes and the organization of the precipitates, while the scattering near Bragg peaks allowed a determination of the distortions of the lattice created by these precipitates.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 488-492  [ doi:10.1107/S0021889805006588 ]

Resolution of small-angle neutron scattering with a refractive focusing optic

D. F. R. Mildner

Synopsis: The analytic expression for the small-angle neutron scattering spectrometer that uses a refractive focusing optic is derived.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 493-500  [ doi:10.1107/S0021889805007442 ]

The use of gradient direction in pre-processing images from crystallization experiments

J. Wilson and I. Berry

Synopsis: This paper discusses methods for improved processing of images in the automated analysis of crystallization experiments for high-throughput X-ray crystallography

Online 13 May 2005


 

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J. Appl. Cryst. (2005). 38, 501-504  [ doi:10.1107/S0021889805007685 ]

An efficient routine for computing symmetric real spherical harmonics for high orders of expansion

A. Kudlicki, M. Rowicka, M. Gilski and Z. Otwinowski

Synopsis: A numerically efficient method of constructing symmetric real spherical harmonic bases is presented. This approach allows for fast and stable computation up to very high order, which can be used in e.g. averaging of non-crystallographic symmetry in protein crystallography or refinement of large viruses in electron microscopy.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 505-511  [ doi:10.1107/S0021889805008319 ]

The derivation of the cellulose microfibril angle by small-angle X-ray scattering from structurally characterized softwood cell-wall populations

K. M. Entwistle, S. J. Eichhorn and N. Navaranjan

Synopsis: A method is presented for the measurement, using small-angle X-ray scattering (SAXS), of the microfibril angle and the associated standard deviation for the cellulose microfibrils in the S2 layer of the cell walls of softwood specimens.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 512-519  [ doi:10.1107/S0021889805009234 ]

Advances in digital topography for characterizing imperfections in protein crystals

J. J. Lovelace, C. R. Murphy, H. D. Bellamy, K. Brister, R. Pahl and G. E. O. Borgstahl

Synopsis: A system which automatically couples digital topography with fine [varphi]-sliced reflection profiling has been developed and applied to cryocrystallography.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 520-527  [ doi:10.1107/S0021889805010034 ]

Intersect distributions of a `dead leaves' model with spherical primary grains

W. Gille

Synopsis: Operating with the pair correlation function, geometric properties and characteristic SAS parameters of a special tightly packed arrangement of hard spheres of constant diameter are investigated. Starting from the SAS correlation function of a hard-particle `dead leaves' model, the distribution density of isotropic uniform random chords, belonging to the connected phase, is determined analytically.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 528-536  [ doi:10.1107/S0021889805009891 ]

The LIESST state of [Fe(pic)3]Cl2.EtOH - the superstructure under continuous irradiation

J. Kusz, D. Schollmeyer, H. Spiering and P. Gütlich

Synopsis: A superstructure induced by a high-spin to low-spin transition is described.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 537-543  [ doi:10.1107/S0021889805010356 ]

Orientation relations between zincblende-, cinnabar- and NaCl-type phases of CdTe under high pressure

H. Sowa

Synopsis: The orientation relations between three phases of CdTe were studied under high pressure using X-ray diffraction. Three different transition mechanisms are discussed.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 544-554  [ doi:10.1107/S0021889805009908 ]

Absolute optical rotation of CsLiB6O10

J. Herreros-Cedrés, C. Hernández-Rodriguez and W. Kaminsky

Synopsis: Determination of the absolute optical rotation of CsLiB6O10 by the TILTER and HAUP techniques is described.

Online 13 May 2005


short communications


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J. Appl. Cryst. (2005). 38, 555-558  [ doi:10.1107/S0021889805010472 ]

Glucose isomerase from Streptomyces rubiginosus - potential molecular weight standard for small-angle X-ray scattering

M. Kozak

Synopsis: Studies of glucose isomerase from Streptomyces rubiginosus by small-angle X-ray scattering indicate that it could be a more stable molecular weight standard for SAXS than bovine serum albumin.

Online 13 May 2005


computer programs


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J. Appl. Cryst. (2005). 38, 559-562  [ doi:10.1107/S0021889805007909 ]

Determination of crystal orientation from micrographs using a MATLAB program

U. Gibson and Y. Kou

Synopsis: Crys.m is a MATLAB routine that combines a micrograph of a crystal with a scaleable, rotatable three-dimensional cage structure to determine the orientation of the crystal axes.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 563-565  [ doi:10.1107/S0021889805008289 ]

Interactive visualization of electron density slices

F. R. N. C. Maia, A. Szöke, W. DeLano and D. van der Spoel

Synopsis: A tool was developed to aid in the visualization of weak or irregular features in electron density which are difficult or impossible to observe using isosurfaces. This tool has been integrated into an existing molecular visualization package, PyMol, making it possible to observe and interact simultaneously with a structure model and the electron density slices.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 566-567  [ doi:10.1107/S0021889805012148 ]

WinXMorph: a computer program to draw crystal morphology, growth sectors and cross sections with export files in VRML V2.0 utf8-virtual reality format

W. Kaminsky

Synopsis: This article presents a Windows application, WinXMorph, with which near reality crystal morphologies are made and exported as virtual reality files in the VRML V2.0 format.

Online 13 May 2005


laboratory notes


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J. Appl. Cryst. (2005). 38, 568-570  [ doi:10.1107/S0021889805008277 ]

Practical implementations for improving the throughput in a manual crystallization setup

C. Biertümpfel, J. Basquin and D. Suck

Synopsis: New tools and an advanced protocol are presented for improving the throughput in manual crystallization using 96-well microplates. The described procedures and devices help to reduce setup time and costs.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 571  [ doi:10.1107/S0021889805010095 ]

Cooler for obtaining crystals

B. Cabric and T. Pavlovic

Synopsis: A design for a modular air cooler (`crystallization comb') installed in a laboratory chamber furnace is presented. The setup allows regulation of a series of crystallization parameters in crucible columns, with the purpose of obtaining crystals.

Online 13 May 2005


computer program abstracts


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J. Appl. Cryst. (2005). 38, 572-573  [ doi:10.1107/S0021889805009337 ]

Fourier3D: visualization of electron density and solvent-accessible voids in small-molecule crystallography

D. M. Tooke and A. L. Spek

Synopsis: The program displays three-dimensional images of Fourier maps and solvent-accessible voids.

Online 13 May 2005


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J. Appl. Cryst. (2005). 38, 574-575  [ doi:10.1107/S0021889805011052 ]

Qs v.1.3: a parallel version of Queen of Spades

N. M. Glykos

Synopsis: A parallel version of Queen of Spades, which encodes an algorithm for a stochastic multidimensional approach to molecular replacement, is presented.

Online 13 May 2005


 

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J. Appl. Cryst. (2005). 38, 576-577  [ doi:10.1107/S0021889805009568 ]

JECP/HOLZ - an interactive computer program for simulation of HOLZ patterns

X. Z. Li

Synopsis: An interactive computer program for the simulation of higher-order Laue zone (HOLZ) line patterns is presented. The program was written in Java using the kinematical approximation and a first-order dynamic correction.

Online 13 May 2005


crystallographers


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J. Appl. Cryst. (2005). 38, 578  [ doi:10.1107/S0021889805010861 ]

Hubert Curien (1924-2005)

Online 13 May 2005


book reviews


 

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J. Appl. Cryst. (2005). 38, 579  [ doi:10.1107/S002188980501246X ]

Crystals that flow. Classic papers from the history of liquid crystals

Online 13 May 2005


 

J. Appl. Cryst. (2005). 38, 580-582

forthcoming meetings and short courses


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