bluuebunny/crossref_metadata_2025 huggingface dataset:
FINAX: a computer program for correcting diffraction angles, refining cell parameters and calculating powder patterns
Authors: Hovestreydt E. R.
Published: July 2002

A computer program is described, whose purpose is the refinement of cell parameters from X-ray or neutron diffraction data. It is of particular use when working with powder diffraction patterns, as it has the possibility of (a) correcting the measured diffraction angles from reference reflections and of (b) calculating a theoretical powder diffractogram, including intensities. A minimum of crystallographic information has to be given and input is partially in free format. E.s.d.'s in cell parameters, as well as in the volume, are calculated. It handles α
1−α
2 splitting and calculates, apart from the theoretical line positions, also a more realistic position of where to expect a given reflection on the film.
The effect of profile-step counting time on the determination of crystal structure parameters by X-ray Rietveld analysis
Authors: Hill R. J. , Madsen I. C.
Published: July 2002

Crystal structure parameters have been obtained for α-Al2O3, β-PbO2 and (Mg, Fe)2SiO4 by Rietveld analysis of Cu Kα X-ray powder diffraction data collected on a conventional diffractometer using counting times ranging from 0.01 to 5 s per step. For all but the 0.01 s data collected on (Mg, Fe)2SiO4 the structural parameters obtained at different counting times are statistically identical at the 3 σ level, and the spread in the values is essentially the same as that obtained by sample repacking at a fixed counting time of 1 s per step. The parameter e.s.d.'s and conventional agreement indices Rwp
and RB
decrease to values limited by residual model errors as the counting time increases, but the goodness-of-fit parameter becomes unacceptably larger than its ideal value of unity. When more than a few thousand counts are accumulated for the maximum step intensity in the diffraction profile a weighting scheme based solely on counting variance is inappropriate and the parameter e.s.d.'s are no longer a reflection of their accuracy.
Simulation of X-ray double-crystal rocking curves at multiple and inhomogeneous heteroepitaxial layers
Authors: Hill M. J. , Tanner B. K. , Halliwell M. A. G. , Lyons M. H.
Published: July 2002

Synchrotron radiation has been used to obtain double-crystal X-ray rocking curves from inhomogeneous layers of GaInAs on InP at a range of wavelengths. The consistency of the lattice-parameter profiles deduced by simulating the rocking curves using the Takagi–Taupin equations is shown to be good. The computational method has been extended to calculate the rocking curves from relatively thick multilayer structures of GaAlAs on GaAs grown by molecular beam epitaxy. This dynamical-theory approach permits the prediction of positions, heights and widths of major and satellite peaks. Results are in excellent agreement with experimental measurements, and by comparing experimental and calculated profiles the structural parameters of the layer can be deduced. The dynamical theory is particularly suitable for calculating the complete rocking curve especially where thick confining layers are present and the computational model is directly applicable to multi-layers with varying layer thicknesses.
Calcium cryolites
Authors: Baggio S. , Massiff G.
Published: July 2002

In aluminium production, the electrolyte is a molten mixture of cryolite, alumina, aluminium fluoride and additives like calcium fluoride. When the electrolyte solidifies several phases appear, some of them known as `calcium cryolites'. In this paper we report the identification, empirical formulas and powder diagrams for three of them: NaF.AlF3.1.50CaF2 (form I); NaF.AlF3.CaF2 (form II); NaF.1.75AlF3.CaF2 (form III). The JCPDS Diffraction File Nos. are 36–1496 for NaF.AlF3.1.5CaF2, 36–1498 for NaF.AlF3.CaF2 and 36–1497 for NaF.1.75AlF3.CaF2.
X-ray topographic study of dislocation around indents on {111} surfaces of indium antimonide
Authors: Surowiec M. R. , Tanner B. K.
Published: July 2002

The dislocation configurations around microindentations on {111} surfaces of InSb have been studied by transmission X-ray topography. In all cases, glide on the B-type {111} planes only occurs. The most extended dislocation loops occur around A-surface indents. Glide occurs on inclined {111} planes and the loops have extended screw segments parallel to the surface. Around B-surface indents dislocations glide predominantly on the ({\bar 1} {\bar 1} {\bar 1}) plane parallel to the surface. The mobility of these dislocations is about two or three times less than the former type. Direct evidence for the formation of edge dislocation barriers from reactions between dislocations gliding in the ({\bar 1} {\bar 1} {\bar 1}) plane is presented.
Computer derivation of the symmetry elements implied in a structure description
Authors: Le Page Y.
Published: July 2002

The space-group symmetry implied in the atomic coordinates of a structure can be reconstructed by deriving the metric symmetry elements of the lattice from the cell data, and finding the location and the glide for corresponding space-group symmetry elements with the same orientation using the list of atomic coordinates. The MISSYM computer program designed along these principles treated correctly the known examples of overlooked symmetry or quasi-symmetry that were submitted to it. As no computer program operating on refined atomic coordinates can prove the presence of extra symmetry in the crystal, the user should scrutinize the experimental evidence and report either a different space group or the existence of pseudo-symmetry whenever extra structural symmetry elements are disclosed by the program. The MISSYM program is part of the NRCVAX system of programs.
Lorentz–polarization factor for correction of diffraction-line profiles
Authors: Yinghua W.
Published: July 2002

The Lorentz–polarization factor (1 + cos22 θ)/sin2
θ cos θ for the integrated intensity of a diffraction line is different from the Lorentz–polarization factor (1 + cos2 2θ)/sin2
θ for a diffraction-line profile; nevertheless, in most of the literature it is being used to correct diffraction-line profiles. The errors introduced in the peak shape and position by use of the Lorentz–polarization factor (1 + cos2 2θ)/sin2
θ cos θ are discussed.
A system for collection and on-line integration of X-ray diffraction data from a multiwire area detector
Authors: Blum M. , Metcalf P. , Harrison S. C. , Wiley D. C.
Published: July 2002

A system for collecting and measuring X-ray diffraction data from protein crystals has been developed for a multiwire area detector. Computer programs run concurrently on two microcomputers, which collect and reduce detector data to integrated intensities. The self-contained system consists of an X-ray area detector, a rotation/oscillation camera, and two microcomputers connected by a high-speed Ethernet network. One microcomputer is dedicated to operation of the detector, control of the camera, and storage of the raw data. The second microcomputer automatically integrates the data as they are collected and allows the user to monitor the quality of data as they are processed. The integration programs are written in Fortran 77 and have been designed to be portable. Additional programs for crystal alignment, detector and camera control, and graphics are written in the C programming language. A description of the system, some characteristics of the detector, and the results of data collection are presented.
Rationale of a quick adjustment method for crystal orientation in oscillation photography. Erratum
Authors: Suh I.-H. , Suh J.-M. , Ko T.-S. , Aoki K. , Yamazaki H.
Published: July 2002

In the paper by Suh, Suh, Ko, Aoki & Yamazaki [J. Appl. Cryst. (1988). 21, 521–523], the penultimate sentence of the Concluding remarks section is in error. The correct sentence is Subtract the deviation in the bottom half from the deviation in the top half to give the correction for the vertical arc: if the result is + Δν
 mm, rotate the vertical arc by Δv
° clockwise, and by Δν
° anticlockwise in the case of −Δν
 mm.
Modeling of Bragg intensity profiles. 1. Allowance for crystal mosaicity
Authors: Laktionov A. V. , Chulichkov A. I. , Chulichkova N. M. , Fetisov G. V. , Pyt'ev Yu. P. , Aslanov L. A.
Published: July 2002

The model of the instrumental function of a four-circle X-ray diffractometer suggested earlier [Chulichkov et al. (1987). Kristallografiya, 32, 1107–1114] is complemented by the introduction of the crystal mosaicity. This improved model is used to develop a method for the reconstruction of the mosaicity function profile f(ω) from the experimental intensity profile I(ω) measured on a diffractometer. The method consists of the reduction of the experimental I(ω) distribution to the form it would have if it were measured on a diffractometer with an instrumental function close to the δ function. The suggested method for determining f(ω) is tested on Si crystals with dislocation densities Nd
= 3 × 1010 and 2 × 1011 m−2.
Lattice parameters and spontaneous strain in AX
2 polytypes: CdI2, PbI2 SnS2 and SnSe2
Authors: Pałosz B. , Salje E.
Published: July 2002

Structural transformations between polytypes of a given material are expected to lead to lattice relaxations. Powder X-ray diffraction of basic AX
2 polytypes of CdI2, PbI2, SnS2 and SnSe2 showed these relaxations for the repetition unit along the stacking axis, conventionally the c axis. No variation of the lattice parameters were detected in the basal plane (001), except for CdI2 where small variations occur also for the a lattice parameter. The tensor of the spontaneous strain has its maximum component e
3 ≲ 12 × 10−4 for SnS2. The powder diffraction pattern and lattice parameters of the phases of CdI2 (2H, 12R, 4H), PbI2 (2H, 12R), SnS2 (2H, 18R, 4H) and SnSe2 (2H, 18R) are given. JCPDS Diffraction File Nos. are: 40-1468 for CdI2-12H; 40–1469 for CdI2-2H; 40-1466 for SnS2-18R, 40–1467 for SnS2-2H; 40–1465 for SnSe2-18R. The other polytypes studied in this paper have data in earlier sets of the PDF.
Schematic diagrams of nucleic acids and protein–nucleic acid complexes
Authors: Lesk V. I. , Lesk A. M.
Published: July 2002

Simplified representations of components of nucleic acids have been designed and implemented as programs integrated with other software that draws schematic diagrams of proteins. Examples illustrating the structures of oligonucleotides, tRNA and a protein–nucleic acid complex indicate the utility of these representations for making intelligible illustrations of complex structures containing nucleic acids.
On the definition and practical use of crystal-based azimuthal angles
Authors: Schwarzenbach D. , Flack H. D.
Published: July 2002

A diffractometer-independent definition of the azimuthal angle ψ of a Bragg reflection is proposed. After completion of intensity measurement, instrument-dependent and partly redundant quantities such as orientation matrix and setting angles may be replaced by ψ, values without loss of information. Data-treatment software, such as absorption- and anisotropic extinction-correction programs, become instrument independent and completely general. Formulae are given to compute ψ for equatorial and non-equatorial diffraction geometries.
Dislocations around scratches and indents on ±(111) surface of gallium arsenide
Authors: Surowiec M. R. , Leipner H. S. , Schreiber J.
Published: July 2002

The dislocation configurations around microscratches and indents on ±(111) surfaces of GaAs single crystals were studied by X-ray transmission topography, scanning electron microscopy in cathodoluminescence mode and high-voltage transmission electron microscopy. Most of the dislocations generated are loops of screw – B(g) or screw –B(g) – screw character gliding on {111} slip planes parallel or inclined to the surface. The irregular shape of the extended loops gliding parallel to the B surface is due to interaction with other loops and apparent motion involving a double kink nucleation mechanism. The exhibited configuration of dislocation loops suggests a cross-slip orientation of the dissociated screw segments. The direction of propagation of dislocations does not depend on the sense of scratching. Grown-in dislocations are surrounded by a cloud of point defects and they are immobile in contrast to dislocations introduced by indentation.
Correction for absorption and beam inhomogeneity in X-ray single-crystal diffractometry: method of analytical integration
Authors: Markov V. T. , Fetisov G. V. , Zhukov S. G.
Published: July 2002

A computational method of absorption correction in X-ray diffractometry for single crystals in the shape of convex polyhedra bathed in an inhomogeneous and in a homogeneous X-ray beam is suggested. An absorption correction is calculated for each reflection of the data set using the measured coordinates of the specimen vertices and the experimentally measured intensity distribution in the primary beam. The program ABSCOR is written in Fortran and may be readily adopted to any four-circle diffractometer and data format. The results of the method described for crystals of different dimensions and different absorption coefficients are given. It is shown that beam inhomogeneity strongly influences the reflection intensity of large non-isometric crystals.
FIT, a computer program for decomposition of powder diffraction patterns and profile analysis of pair correlation functions
Authors: Petkov V. , Bakaltchev N.
Published: July 2002

FIT is an interactive computer program for fitting analytical models to powder diffraction patterns and to pair correlation functions. FIT has been written in Turbo C and runs on IBM XT/AT or compatible personal computers.
Time-resolved two-dimensional observation of the change in X-ray diffuse scattering from an alloy single crystal using an imaging plate on a synchrotron-radiation source
Authors: Iwasaki H. , Matsuo Y. , Ohshima K. , Hashimoto S.
Published: July 2002

Through the high sensitivity of an area-detector Imaging Plate and the high brilliance of synchrotron radiation, changes in two-dimensional intensity distribution of X-ray diffuse scattering from an AgZn single-crystal having the B2-type structure were observed successively during the structural transition from the β′ phase to the ζ phase. It has been shown in a series of patterns taken at a time interval of 600 s that a diffuse intensity sheet extending parallel to the (111) relplane gradually loses its intensity without a precursive modulation while weak diffraction spots from the nuclei of the ζ phase appear superimposed on the sheet with a definite positional relation to the diffraction spots from the β′ phase. Promising aspects as well as the limits of the method applied to time-resolved measurements of structural changes are discussed.
Small-angle-scattering determination of the microstructure of porous silica precursor bodies
Authors: Long G. G. , Krueger S. , Jemian P. R. , Black D. R. , Burdette H. E. , Cline J. P. , Gerhardt R. A.
Published: July 2002

Small-angle X-ray and small-angle neutron scattering measurements were carried out on a series of porous silica precursor (unsintered) bodies with different starting chemistries. The samples were prepared from mixtures containing 10 to 30 wt% colloidal silica sol and 90 to 70 wt% potassium silicate. Particle-size distributions were derived from the data using a maximum-entropy technique. Scattering data from the porous silica samples are especially suitable for such an analysis because the colloidal particles and clusters and aggregates of these particles are verified in detail to be spherical, and the scattering instrument use for this study covered the entire range of sizes in this material and was very well calibrated. It was found that the lower the amount of colloidal silica, the broader the size distribution of the silica aggregates.
X-ray diffraction study of lithium hydrazinium sulfate and lithium ammonium sulfate crystals under a static electric field
Authors: Sebastian M. T. , Becker R. A. , Klapper H.
Published: July 2002

X-ray diffraction studies are made on proton conducting polar lithium hydrazinium sulfate and ferroelectric lithium ammonium sulfate. The X-ray rocking curves recorded with in situ electric field along the polar b axis of lithium hydrazinium sulfate (direction of proton conductivity) show a strong enhancement of the 0k0 diffraction intensity. The corresponding 0k0 X-ray topographs reveal extinction contrast consisting of striations parallel to the polar axis. They disappear when the electric field is switched off. The effect is very strong in 0k0 but invisible in h0l reflections. It is present only if the electric field is parallel to the polar axis b. This unusual X-ray topographic contrast is correlated with the proton conduction. It is supposed that, under electric field, an inhomogeneous charge distribution develops, distorting the crystal lattice. Similar experiments on lithium ammonium sulfate also show contrast variations, but of quite different behaviour than before. In this case they result from changes of the ferroelectric domain configuration under electric field.
The evaluation of transmission factors and their first derivatives with respect to crystal shape parameters
Authors: Blanc E. , Schwarzenbach D. , Flack H. D.
Published: July 2002

Methods, implemented into a computer program (LSABS), are described which calculate transmission factors and their first derivatives with respect to the positions of the faces of a convex polyhedral monocrystal. Both Gaussian and analytical integration procedures are considered in detail. LSABS has been implemented as a module of the
Xtal
system of programs. It functions independently of the instrument used to collect the intensity data. Test results obtained with this program are compared with standard literature values. Correlation coefficients of an absorption-corrected intensity data set of calcite, CaCO3 are reported. The need for transmission factor derivatives in the refinement of crystal shape and in the elimination of correlated absorption-corrected structure amplitudes is explained.
The inertia-equivalent ellipsoid: a link between atomic structure and low-resolution models of small globular proteins determined by small-angle X-ray scattering
Authors: Müller J. J. , Schrauber H.
Published: July 2002

Low-resolution three-parameter models of the shape of a biopolymer in solution can be determined by a new indirect method from small-angle X-ray scattering without contrast-variation experiments. The basic low-resolution model employed is a triaxial ellipsoid – the inertia-equivalent ellipsoid (IEE). The IEE is related to the tensor of inertia of a body and the eigenvalues and eigenvectors of this tensor can be calculated directly from the atomic coordinates and from the homogeneous solvent-excluded body of a molecule. The IEE defines a mean molecular surface (like the sea level on earth) which models the molecular shape adequately if the IEE volume is not more than 30% larger than the dry volume of the molecule. Approximately 10 to 15% of the solvent-excluded volume is outside the ellipsoid; the radii of gyration of the IEE and of the homogeneous molecular body are identical. The largest diameter of the IEE is about 5 to 15% (~0.2–0.8 nm) smaller than the maximum dimension of globular molecules with molecular masses smaller than 65000 daltons. From the scattering curve of a molecule in solution the IEE can be determined by a calibration procedure. 29 proteins of known crystal structure have been used as a random sample. Systematic differences between the axes of the IEE, calculated directly from the structure, and the axes of the scattering-equivalent ellipsoids of revolution, estimated from the scattering curve of the molecule in solution, are used to derive correction factors for the axial dimensions. Distortions of model dimensions of 20 to 40% (up to 1 nm), caused by misinterpretation of scattering contributions from electron density fluctuations within the molecule, are reduced to a quarter by applying these correction factors to the axes of the scattering-equivalent ellipsoids of revolution. In a computer experiment the axes of the inertia-equivalent ellipsoids have been determined for a further nine proteins with the same accuracy. The automated estimation of the IEE from the scattering curve of a molecule in solution is realized by the Fortran77 program AUTOIEE.
The lens equation for Bragg diffraction optics. The general case of asymmetrical reflection
Authors: Chukhovskii F. N. , Krisch M.
Published: July 2002

The lens equation for Bragg diffraction of monochromatic X-rays and neutrons in the case of a cylindrically curved crystal is derived for the general Bragg- and Laue-case geometries. The resulting equation is identical to the formula for polychromatic focusing only in the limits of symmetrical reflection and/or in Rowland geometry.
Step size, scanning speed and shape of X-ray diffraction peak
Authors: Wang H.
Published: July 2002

The influences of step size and scanning speed on the shape of a single X-ray diffraction (XRD) peak are analyzed quantitatively. For this purpose, it is assumed that XRD peak shapes are a mixture of Cauchy and Gauss curves. Six equations are established for the calculation of position, maximum intensity and full width at half-maximum (FWHM) errors caused by step size and two for the FWHM errors caused by counting statistics. The ratio of step size to FWHM is proposed as the shape-perfect coefficient of the XRD peak. From these equations and the relationship between the FWHM and the integral width of a peak based on the pseudo-Voigt function or Voigt function, three basic elements of a single symmetric XRD peak (peak position, maximum intensity and FWHM) can be refined. The optimum step size and scanning time can also be set from them.
Diffuse X-ray scattering in potassium lithium sulfate, KLiSO4
Authors: Welberry T. R. , Glazer A. M.
Published: July 2002

Detailed diffuse X-ray scattering patterns of potassium lithium sulfate, KLiSO4, in sections normal to [00.1], have been recorded using a position-sensitive detector system. A number of distinctive diffuse features are observed including elongated diffuse peaks near Bragg-peak positions, bands of weaker intensity running normal to a*, b* etc. and darker regions relatively free from scattering in the shape of hexagons and a six-pointed star. Monte Carlo simulation of simple potential models has been carried out in an attempt to explain this scattering and also the observation from Bragg analysis [Schulz, Zucker & Frech (1985). Acta Cryst. B41, 21–26] that mean-square atomic displacements for the apical O(1) atom show a pronounced threefold symmetry. A simple potential, in which harmonic (Hookes law) springs with lengths equal to the observed average bond distances are assumed between the different types of nearest-neighbour atom pairs, is able to account qualitatively for all of the observed diffraction features but gives quite isotropic atomic displacement distributions. A second model is described, which assumes that a small number of point defects are present, in which the potassium sites are occasionally occupied by lithium. The distortion of the very flexible LiO4 framework around such defects can account for the trigonal shape of the O(1) sites while still giving diffuse diffraction patterns similar to those from the simpler harmonic model.
Mixing Symmetric and Oblique Bragg Reflections in Rigid Channel-Cut Crystals
Authors: Hart M. , Koga T. , Takano Y.
Published: July 2002

Because the Bragg angle and Darwin range of total reflection in symmetric and oblique Bragg reflections vary with the angle between the Bragg planes and the crystal surface, it is generally believed that the resulting mismatch causes a loss of intensity in monolithic channel-cut crystals that is unacceptable in practice. It has been discovered that in the unique case of the 220 Bragg reflection from germanium no mismatch occurs, so that oblique and symmetric reflections can be mixed in one rigid channel-cut crystal. The results are valid for both X-ray and neutron channel-cut monochromators.
Orientation Analysis of Bulk YBCO from Incomplete Neutron Diffraction Data
Authors: Chateigner D. , Wenk H.-R. , Pernet M.
Published: July 2002

Highly incomplete pole figures of a magnetic-field-aligned melt-textured superconducting sample of the Y–Ba–Cu–O system were measured by neutron diffraction. The orientation distribution of the main superconducting 123 and a minor 211 phase have been derived with the WIMV algorithm. The 123 phase is strongly textured with a (001) maximum around 22 times that of a random distribution (m.r.d.) and a texture index of 30. There are two orientation components present that have no apparent relationship with the applied magnetic field. The texture of the 211 phase is weak, with a maximum of 1.7 m.r.d. The textures of the two phases appear to be correlated.
Outlier Treatment in Data Merging
Authors: Blessing R. H.
Published: July 2002

Experience with a variety of diffraction data-reduction problems has led to several strategies for dealing with mismeasured outliers in multiply measured data sets. Key features of the schemes employed currently include outlier identification based on the values y
median = median(|Fi
|2), σ
median = median[σ(|Fi
|2)], and |Δ|median = median(|Δi
|) = median[||Fi
|2-median (|Fi
|2)|] in samples with i = 1, 2 ..... n and n ≥ 2 measurements; and robust/resistant averaging weights based on values of |zi
| = |Δi
|/max{σ
median, |Δ|median[n/(n−1)]1/2}. For outlier discrimination or down-weighting, sample median values have the advantage of being much less outlier-based than sample mean values would be.
The Application of Resonant Scattering Techniques toAb InitioStructure Solution from Powder Data using SrSO4as a Test Case
Authors: Burger K. , Cox D. , Papoular R. , Prandl W.
Published: July 2002

The application of resonant (anomalous) scattering techniques toab initiostructure solution from powder data is demonstrated for the compound SrSO4. This material is orthorhombic, in space groupPnma(a = 8.359,b = 5.351,c = 6.869 Å,Z = 4), with 11 variable atomic positional parameters, and gives a fairly complex powder pattern with many overlapping peaks. Accurate high-resolution synchrotron X-ray powder diffraction data were obtained at three energies: 14, 225 and 5133 eV below the SrKedge. From combinations of two of the three data-sets, partial Patterson densities were derived and used to phase the 71 uniquely resolved reflections, allowing a complete solution of the rest of the structure. Maximum entropy methods were found to be far superior to standard Fourier methods in the reconstruction of the electron-density distribution. The techniques of data collection, analysis and phase determination required for resonant scattering experiments of this type are described in detail.
X-ray diffraction study of concentration depth profiles of binary alloy coatings during thermal diffusion: application to brass coating
Authors: Bolle B. , Tidu A. , Heizmann J. J.
Published: July 2002

Using the Houska method based on X-ray diffraction-line profile analysis, new mathematical treatments are proposed to compute directly the concentration depth profile of thin films obtained by diffusion. As an example, concentration depth profiles of a brass layer have been studied during the thermal diffusion process. This nondestructive method is fast (a few minutes) and allows the sample to be used for complementary analysis if necessary.
A new CuKα2-elimination algorithm
Authors: Dong C. , Chen H. , Wu F.
Published: July 2002

This paper presents a new algorithm to remove the CuKα2profile in X-ray powder diffraction patterns. Previous algorithms for α2elimination can be divided into two categories. The first category assumes the shape identity of the α1and α2components. The second category uses parameters by fitting experimental data. The first category is not accurate and the second one is instrument-dependent. The algorithm presented here uses the CuKα emission profile obtained from monolithic double-crystal measurements. Therefore, it is more accurate and less instrument-dependent than the previous methods. This algorithm has been tested and applied in software for diffraction data processing. The present method can be extended to removeKα2lines of other radiations.
The dislocation model of strain anisotropy in whole powder-pattern fitting: the case of an Li–Mn cubic spinel
Authors: Ungár T. , Leoni M. , Scardi P.
Published: July 2002

Anisotropic strain broadening in X-ray or neutron powder diffraction can cause severe difficulties in whole powder-pattern fitting and Rietveld structure refinement. Several phenomenological models have been proposed to deal with this problem. These, however, lack physically sound bases. In the present work the dislocation-based model of strain anisotropy is applied in the Fourier formalism of profile fitting. It is shown that the anisotropic contrast of dislocations can fully account for strain anisotropy. A few physically sound parameters, namely the average dislocation density, the average coherent domain size, the dislocation arrangement parameter and the dislocation contrast factors, enable a perfect profile fitting to the powder pattern of a cubic Li–Mn spinel obtained at the Daresbury synchrotron storage ring.
FINDNCS: a program to detect non-crystallographic symmetries in protein crystals from heavy-atom sites
Authors: Lu Guoguang
Published: July 2002

In order to facilitate applications of averaging techniques in the MIR/MAD procedure, a program,FINDNCS, which automatically identifies non-crystallographic symmetry (NCS) from heavy-atom sites, has been developed. The program outputs the NCS operations (a rotation matrix and a translation vector), the corresponding root-mean-square (r.m.s.) deviations of heavy-atom sites, polar angles and screw translations, and writes coordinates of matching sites in Protein Data Bank (PDB) format. The program has an interface with the graphics programO[Joneset al. (1991).Acta Cryst.A47, 110–119] so that the NCS operations can be displayed automatically. In the test examples, all the correct NCS operations were identified and were above the noise solutions.
Measurement of single-crystal elastic constants by neutron diffraction from polycrystals
Authors: Howard C. J. , Kisi E. H.
Published: July 2002

The relationships of diffraction averaged elastic compliances for an ideally random polycrystal to the single-crystal elastic compliances are given, within the Reuss approximation, for crystal systems with orthorhombic and higher symmetry. For anisotropic materials, these diffraction elastic compliances are dependent on the reflection indexhkl. Expressions for the conventional elastic constants (Young's modulus, Poisson's ratio) are also given. A connection is made to the `X-ray elastic constants' used for diffraction-based measurements of residual stress. The relationships are used to calculate diffraction averaged constants for comparison with neutron diffraction data recorded from samples under applied uniaxial stress. The Reuss approximation works well for materials with the capacity for plastic deformation, such as metals and transformation toughening ceramics, whereas for other materials the Voigt–Reuss–Hill approximation gives better results. Based on the given relationships and experimental determinations of the diffraction elastic compliances for polycrystalline materials, a method is developed for determining the single-crystal elastic constants. The method for estimating single-crystal compliances is demonstrated here by application to extant data on Ni–Cr–Fe and Ti–6 wt% Al–4 wt% V alloys, and new measurements on cubic zirconia. It has been applied very recently [Kisi & Howard (1998).J. Am. Ceram. Soc.81, 1682–1684] to determine the previously unknown elastic constants for a tetragonal zirconia.
Adaptation of the Rietveld method to the characterization of the lamellar microstructure of polymers. 2. Influence of a tilt of chain axesversusthe normal to basal planes of crystalline lamellae
Authors: Dupont O. , Ivanov D. A. , Jonas A. M. , Legras R.
Published: July 2002

In a previous paper [Dupont, Jonas & Legras (1997).J. Appl. Cryst.30, 921–931], a variant of the Rietveld method was applied to the characterization by X-ray scattering (powder diffractometry) of disordered and small crystals as found in semicrystalline polymers. In the present study, a new version of the model is described, which is designed to take into account the possible existence of a non-zero tilt angle (ψ) of the chain axesversusthe large faces of the lamellar crystals. Fits of this model to the diffractograms of various samples of cold-crystallized PEEK [poly(ether-ether-ketone)] and of a monodisperse PEEK oligomer are presented. For the oligomer, the fits converged only towards ψ = 0°. For the polymers, two equivalent solutions were found, one with thick lamellae and ψ = 0°, another with thinner lamellae and ψ = 20°. Models with and without chain tilt give similar goodness-of-fit parameters, indicating that results coming from other techniques than X-ray diffractometry are required in order fully to characterize the dimensions and shape of crystals in isotropic polymer samples. Comparing the present values with results obtained by such other techniques suggests the existence of a tilt angle for cold-crystallized PEEK samples.
DATPROC9: a data-processing program based on a new extension of the learnt-profile method
Authors: Gałdecka E.
Published: July 2002

The main aim realised by theDATPROC9 program is to process the data recorded on a KM4 diffractometer (Kuma Diffraction) to obtain aname.hkl collection of intensities for a crystal-structure determination, using a version of the new extension of the learnt-profile method, selected from among the following: `basic learnt profile', `simple learnt profile' and `convolution model'. The model function to be used for approximation of the data at the final stage of calculations is derived during preliminary stages. The basic shape function(s) used in the selected method is (are) displayed on the screen, and some details of modelling and notes on the efficiency of the data processing are given in special text files produced at every stage. One can also view on screen intensity plots of the measured profiles and their models. One may also process the data with `no profile fitting', or using a simpler data-refinement method (`simple smoothing').
Use of an open-flow helium cryostat for macromolecular cryocrystallography
Authors: Hanson B. Leif , Martin Anthony , Harp Joel M. , Parrish Damon A. , Bunick Christopher G. , Kirschbaum Kristin , Pinkerton A. Alan , Bunick Gerard J.
Published: July 2002

A helium cryostat developed at the University of Toledo has recently been described by Hardie, Kirschbaum, Martin & Pinkerton [J. Appl. Cryst.(1998),31, 815–817]. This helium cooling system has now been tested on macromolecules, using crystals of chicken egg lysozyme and sperm whale myoglobin. Phase changes in terbium vanadate crystals indicate that temperatures delivered by the cryostat were less than 33 K. Unit-cell contraction in the protein crystals is consistent with the previously reported He data. Large crystals approaching suitability for neutron diffraction studies were successfully flash-cooled and a large crystal of lysozyme was rescued for data collection after undergoing a cycle of macromolecular crystal annealing (MCA) following poor flash-cooling. Comparison of diffraction data from sperm whale myoglobin crystals collected in both He and N2showed a 23% lower overallBfactor for the He data. The results of these studies show that this device might be an especially useful adjunct both for neutron diffraction studies and at high-intensity synchrotron X-ray sources, in addition to its use in the standard macromolecular crystallography laboratory.
High-resolution transmission electron microscopy study of the φ′- and δ-AlON spinel phases of the pseudo-binary section AlN–Al2O3
Authors: Tabary P. , Servant C. , Guymont M.
Published: July 2002

A previously proposed structural model [Tabary & Servant (1999).J. Appl. Cryst.32, 253–272] for the φ′- and δ-AlON spinel phases, which allows for the double modulation of composition and displacement of cations and anions and which describes both phases and their relationships to the γ-AlON spinel phase, is here supported by high-resolution electron microscopy observations.
Small-angle scattering intensity behaviours of cylindrical, spherical and planar lamellae
Authors: Ciccariello Salvino , Sobry Roger
Published: July 2002

Analytical asymptotic expressions for the small-angle scattering intensities of cylindrical, spherical and planar lamellar grains are determined. Denoting the lamellar spacing byDand the number of lamellae byN, it is found that in the corresponding Porod plots, the positions of the main peaks, whatever the shape, are nearly given by 2k\pi/D, wherekis a positive integer. At a fixed number of lamellar grains, the heights of the main peaks in the three cases increase withNasN3,N4andN2, respectively. The satellite peaks are much more structured for cylindrical and spherical lamellae than for planar ones. The momentum-transfer (h) range in which the asymptotic expressions turn out to be accurate is h\ge 2\pi/ND.
Laboratory X-ray powder diffraction: a comparison of different geometries with special attention to the usage of the CuKα doublet
Authors: Oetzel Martin , Heger Gernot
Published: July 2002

In a laboratory X-ray powder diffraction study, the evaluation of the patterns of three Bragg–Brentano powder diffractometers with different monochromator geometries has been undertaken. For the measurements on each diffractometer, the standard reference material SRM 640 (silicon) and the corundum samples SRM 674a and SRM 1976 have been used. In each case, the peak profiles were fitted with a split Pearson VII function and the FWHM (full width at half-maximum) parameters and exponentmwere determined for the left (lower 2θ) and the right (higher 2θ) sides of the Bragg peaks. It was found that there is a strong dependence of both the FWHM and the exponentmon the diffraction angle for the two configurations that included monochromators, whereas nearly constant values ofmwere found for the geometrically simplest diffractometer working without a monochromator. Finally, the two components of the CuKα doublet show systematically different peak profiles. There is a clear difference not only concerning the FWHM, which becomes more obvious at higher 2θ values, but also in the course ofmwith respect to the diffraction angle for the left and the right tails of the powder reflections. This is the main reason for the difficulties inKα2stripping and also in single-line-profile analysis when using theKα doublet. Therefore, it is not surprising that this phenomenon, which can be explained by Heisenberg's uncertainty principle, does affect the reliability (represented by standardRvalues) of structure refinement by the Rietveld method.
Collection of very low resolution protein data
Authors: Miller Stephen T. , Genova John D. , Hogle James M.
Published: July 2002

Simple modifications to a MAR 345 detector which facilitate the collection of very low resolution data are described. With these modifications, the lowest order reflections from a poliovirus crystal (c= 377.1 Å) were observed, and measurement of all reflections in typical protein cells should be routine.
Bare-core approximation: a useful approach to SAS data of block copolymer micelles
Authors: Pleštil J.
Published: July 2002

A middle part of small-angle scattering curves of block copolymer micelles can frequently be described satisfactorily by the scattering function of homogeneous spherical particles (bare-core approximation). This makes it possible to easily determine structure characteristics (mean radius, polydispersity, volume, mass) of the micelle core. Thus, information about the internal structure of the core/corona micellar particles can be obtained without using co-polymers with labelled blocks. Though not universal, this approach is applicable to numerous micellar systems including those formed by hydrogenous copolymers in deuterated solvents. The approach can be also used if the relative excess scattering amplitudes of the core and corona are not a priori known, e.g., in studies of solubilization phenomenon.
TOP: a new method for protein structure comparisons and similarity searches
Authors: Lu Guoguang
Published: July 2002

In order to facilitate the three-dimensional structure comparison of proteins, software for making comparisons and searching for similarities to protein structures in databases has been developed. The program identifies the residues that share similar positions of both main-chain and side-chain atoms between two proteins. The unique functions of the software also include database processingviaInternet- and Web-based servers for different types of users. The developed method and its friendly user interface copes with many of the problems that frequently occur in protein structure comparisons, such as detecting structurally equivalent residues, misalignment caused by coincident match of Cαatoms, circular sequence permutations, tedious repetition of access, maintenance of the most recent database, and inconvenience of user interface. The program is also designed to cooperate with other tools in structural bioinformatics, such as the 3DB Browser software [Prilusky (1998).Protein Data Bank Q. Newslett.84, 3–4] and the SCOP database [Murzin, Brenner, Hubbard & Chothia (1995).J. Mol. Biol.247, 536–540], for convenient molecular modelling and protein structure analysis. A similarity ranking score of `structure diversity' is proposed in order to estimate the evolutionary distance between proteins based on the comparisons of their three-dimensional structures. The function of the program has been utilized as a part of an automated program for multiple protein structure alignment. In this paper, the algorithm of the program and results of systematic tests are presented and discussed.
Position-sensitive analysis in curved-crystal three-axis neutron spectrometry (quasielastic scattering case)
Authors: Stoica A. D. , Popovici M. , Yelon W. B. , Berliner R.
Published: July 2002

The use of bent perfect crystals in focusing three-axis neutron spectrometry with position-sensitive detection (PSD) is analyzed on the basis of a phase-space theory. With PSD, the usual sequential scans are replaced by simultaneous scans. The case of high resolution in energy transfer is considered in detail. With commercial thin silicon wafers, the achievable resolutions are in the 10–150 µeV range, depending on neutron energy. Resolutions around 10 µeV are obtained on the peak of cold-source spectra. To take advantage of the possibilities offered by silicon wafers, PSD with spatial resolution well below 1 mm will be needed. With PSD analysis, a new kind of focusing exists that allows the thickness of bent perfect analyzer crystals to be increased, providing an intensity gain at no resolution loss. With multilamella assemblies a gain in count rate by the number of lamellae in the packet is achievable. Results of a demonstration experiment are presented, confirming that under the right conditions, a multilamella analyzer may resemble a single bent wafer, the individual curves of many wafers having been combined to provide the intensity gain.
Interaction of polymer with clays
Authors: Lal J. , Auvray L.
Published: July 2002

Normally synthetic well defined monodisperse discotic laponite clays are known to form a gel phase at mass concentrations as low as a few percent in distilled water. Hydrosoluble polymer polyethylene oxide was added to this intriguing clay system, it was observed that it either prevents gelation or slows it down extremely depending on the polymer weight, concentration or the laponite concentration. Small Angle Neutron scattering (SANS) was used to study these systems because only by isotopic labelling can the structure of the adsorbed polymer layers be determined. The contrast variation technique is specifically used to determine separately the different partial structure factors of the clay and polymer. In this way the signal of the adsorbed chains is separated from the signal of the free chains.
Small-angle neutron scattering investigation of deuteride (hydride) precipitation and decomposition in single-crystal Pd
Authors: Chen W.C. , Heuser B.J. , King J.S.
Published: July 2002

Small-angle neutron scattering (SANS) measurements of deuteride formation and decomposition in single crystal Pd have been performed. The purpose of this work was to determine and compare the particle morphology during deuteride precipitation and reversion, with the overall goal of developing a model for the pressure hysteresis known to exist in the Pd-H system. Anisotropic Porod scattering at low Q was observed as the samples were driven well into the two-phase region from either solid solution (the α →α' transformation) or from 100% α' (the 'α →α reversion). This scattering is attributed to the formation of large, presumably semi-coherent or completely incoherent, tens-of-microns thick plates on well-defined habit planes. The orientation and dispersion of these larger plates was different for deuteride formation and decomposition: a very coarse dispersion on the {110}α habit plane developed during deuteride formation, while a much finer dispersion on the {100}α' habit plane occurred during deuteride reversion from the 100% deuteride phase. The latter orientation is consistent with the system selecting the habit plane orthogonal to the softest host direction to minimize the elastic accommodation energy of the precipitates. We suspect the {110}α' habit plane observed during deuteride formation is related to large over-pressure loading conditions. An isotropic SANS response from plates with thicknesses of 20 to 30 Å was also observed during deuteride formation and reversion. These plates are thought to act as (coherent) precursors to the large plate formation.
SAXS, SANS and X-ray crystallography as complementary methods in the study of biological form and function
Authors: Forstner M.
Published: July 2002

X-ray crystallography is the single most powerful method for the determination of accurate and precise macromolecular structures. The study of macromolecular motions, however, is, despite some successes with time-resolved crystallography not within the realms of the method. Further, the study of large macromolecular complexes sometimes poses tremendous problems of various kinds for x-ray crystallography and many laboratories approach large structures by solving individual domains. We herein present two examples employing small-angle x-ray and/or neutron scattering (SAXS, SANS) to study (i) conformational changes, and (ii) protein-lipid complexes complementing information from x-ray crystallography. The structural changes of creatine kinase upon substrate binding were investigated as an example of conformational changes not comprehensible from crystallography in the absence of crystal structures of the substrate-ligated enzyme. We also present studies of apolipoprotein E, reconstituted with lipid, in which a combined approach using SAXS/SANS, x-ray crystallography and other techniques yields a model of the complex not accessible by either of the methods alone.
Instrumental line shapes in neutron powder diffraction with focusing monochromators
Authors: Stoica A. D. , Popovici M. , Yelon W. B.
Published: July 2002

The optics of neutron powder diffractometers with bent-crystal monochromators is considered with respect to the computation of instrumental line shapes, accounting for second-order aberrations. A procedure of Monte Carlo simulation of instrumental line shapes has been developed. An analytical approximation of these shapes is described. Computational results for the case of the MURR diffractometer with position-sensitive detection and a focusing silicon monochromator are presented.