Journal of Applied Crystallography
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Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.enCopyright (c) 2017 International Union of Crystallography2017-10-01International Union of CrystallographyInternational Union of Crystallographyhttp://journals.iucr.orgurn:issn:1600-5767Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.text/htmlJournal of Applied Crystallography, Volume 50, Part 5, 2017textweekly62002-02-01T00:00+00:005502017-10-01Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallography1245urn:issn:1600-5767med@iucr.orgOctober 20172017-10-01Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
//journals.iucr.org/j/issues/2017/05/00/isscontsbdy.html
Still imageForm factor of any polyhedron: a general compact formula and its singularities
http://scripts.iucr.org/cgi-bin/paper?fs5152
A general and compact formula is established for the form factor of any polyhedron, which involves only the apex coordinates and the apex connections. For large diffusion vector q, the form factor behaves like q−3 for generic directions, but it exhibits q−2 singularities in the directions perpendicular to the edges and q−1 singularities in the directions normal to the faces. General results are established for these singularities. Using a Python implementation, illustrative examples are discussed. The generality of the formula and of its singularities are likely to be important for any discussion of scattering from polyhedral particles.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Croset, B.2017-08-09doi:10.1107/S1600576717010147International Union of CrystallographyA compact and general formula for the form factor of any polyhedron is given and its singularities are discussed, together with illustrative examples.ENX-ray diffractionform factorspolyhedrananoparticlesA general and compact formula is established for the form factor of any polyhedron, which involves only the apex coordinates and the apex connections. For large diffusion vector q, the form factor behaves like q−3 for generic directions, but it exhibits q−2 singularities in the directions perpendicular to the edges and q−1 singularities in the directions normal to the faces. General results are established for these singularities. Using a Python implementation, illustrative examples are discussed. The generality of the formula and of its singularities are likely to be important for any discussion of scattering from polyhedral particles.text/htmlForm factor of any polyhedron: a general compact formula and its singularitiestext5502017-08-09Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers12451255Applications of dynamical theory of X-ray diffraction by perfect crystals to reciprocal space mapping
http://scripts.iucr.org/cgi-bin/paper?vh5077
The classical dynamical theory of X-ray diffraction is expanded to the special case of transversely restricted wavefronts of the incident and reflected waves. This approach allows one to simulate the two-dimensional coherently scattered intensity distribution centred around a particular reciprocal lattice vector in the so-called triple-crystal diffraction scheme. The effect of the diffractometer's instrumental function on X-ray diffraction data was studied.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Punegov, V.I.Pavlov, K.M.Karpov, A.V.Faleev, N.N.2017-08-09doi:10.1107/S1600576717010123International Union of CrystallographyThe dynamical theory of X-ray diffraction has been developed for spatially restricted beams. This approach allows one to calculate rocking curves as well as reciprocal space maps for both transmitted and reflected coherent wavefields.ENX-ray dynamical diffraction theoryreciprocal space mapstransversely restricted wavefrontsinstrumental functionsThe classical dynamical theory of X-ray diffraction is expanded to the special case of transversely restricted wavefronts of the incident and reflected waves. This approach allows one to simulate the two-dimensional coherently scattered intensity distribution centred around a particular reciprocal lattice vector in the so-called triple-crystal diffraction scheme. The effect of the diffractometer's instrumental function on X-ray diffraction data was studied.text/htmlApplications of dynamical theory of X-ray diffraction by perfect crystals to reciprocal space mappingtext5502017-08-09Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers12561266Three-dimensional texture visualization approaches: applications to nickel and titanium alloys
http://scripts.iucr.org/cgi-bin/paper?po5097
This paper applies the three-dimensional visualization techniques explored theoretically by Callahan, Echlin, Pollock, Singh & De Graef [J. Appl. Cryst. (2017), 50, 430–440] to a series of experimentally acquired texture data sets, namely a sharp cube texture in a single-crystal Ni-based superalloy, a sharp Goss texture in single-crystal Nb, a random texture in a powder metallurgy polycrystalline René 88-DT alloy and a rolled plate texture in Ti-6Al-4V. Three-dimensional visualizations are shown (and made available as movies as supplementary material) using the Rodrigues, Euler and three-dimensional stereographic projection representations. In addition, it is shown that the true symmetry of Euler space, as derived from a mapping onto quaternion space, is described by the monoclinic color space group Pcc in the Opechowski and Guccione nomenclature.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Callahan, P.G.Echlin, M.P.Stinville, J.C.Pollock, T.M.Singh, S.Ram, F.De Graef, M.2017-08-09doi:10.1107/S1600576717010470International Union of CrystallographyThis paper applies three-dimensional visualization techniques to synthetic and experimentally acquired material textures (random, cube and Goss texture components) and illustrates how three-dimensional visualization can be used to gain insight about orientation distribution functions and orientation relations. The intrinsic symmetry of the Euler orientation representations is considered in detail and it is shown that a monoclinic magnetic space group properly describes the symmetry of Euler space.ENtexture representationthree-dimensional visualizationfundamental zonesRodrigues vectorsThis paper applies the three-dimensional visualization techniques explored theoretically by Callahan, Echlin, Pollock, Singh & De Graef [J. Appl. Cryst. (2017), 50, 430–440] to a series of experimentally acquired texture data sets, namely a sharp cube texture in a single-crystal Ni-based superalloy, a sharp Goss texture in single-crystal Nb, a random texture in a powder metallurgy polycrystalline René 88-DT alloy and a rolled plate texture in Ti-6Al-4V. Three-dimensional visualizations are shown (and made available as movies as supplementary material) using the Rodrigues, Euler and three-dimensional stereographic projection representations. In addition, it is shown that the true symmetry of Euler space, as derived from a mapping onto quaternion space, is described by the monoclinic color space group Pcc in the Opechowski and Guccione nomenclature.text/htmlThree-dimensional texture visualization approaches: applications to nickel and titanium alloystext5502017-08-09Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers12671279Nanoparticle size distribution quantification: results of a small-angle X-ray scattering inter-laboratory comparison
http://scripts.iucr.org/cgi-bin/paper?ge5041
This paper presents the first worldwide inter-laboratory comparison of small-angle X-ray scattering (SAXS) for nanoparticle sizing. The measurands in this comparison are the mean particle radius, the width of the size distribution and the particle concentration. The investigated sample consists of dispersed silver nanoparticles, surrounded by a stabilizing polymeric shell of poly(acrylic acid). The silver cores dominate the X-ray scattering pattern, leading to the determination of their radius size distribution using (i) the generalized indirect Fourier transformation method, (ii) classical model fitting using SASfit and (iii) a Monte Carlo fitting approach using McSAS. The application of these three methods to the collected data sets from the various laboratories produces consistent mean number- and volume-weighted core radii of Rn = 2.76 (6) nm and Rv = 3.20 (4) nm, respectively. The corresponding widths of the lognormal radius distribution of the particles were σn = 0.65 (1) nm and σv = 0.71 (1) nm. The particle concentration determined using this method was 3.0 (4) g l−1 or 4.2 (7) × 10−6 mol l−1. These results are affected slightly by the choice of data evaluation procedure, but not by the instruments: the participating laboratories at synchrotron SAXS beamlines, commercial and in-house-designed instruments were all able to provide highly consistent data. This demonstrates that SAXS is a suitable method for revealing particle size distributions in the sub-20 nm region (at minimum), out of reach for most other analytical methods.Copyright (c) 2017 Brian R. Pauw et al.urn:issn:1600-5767Pauw, B.R.Kästner, C.Thünemann, A.F.2017-08-18doi:10.1107/S160057671701010XInternational Union of CrystallographyAn extensive round robin experiment between small-angle X-ray scattering laboratories has delivered a global uncertainty estimate for the measurands of a nanoparticle dispersion. Irrespective of the instrument pedigree, the distribution mean, width and volume fraction could be determined with an accuracy of 1, 10 and 10%, respectively.ENsmall-angle scatteringaccuracymethodologysilver nanoparticlespoly(acrylic acid)SASfitMcSASinverse Fourier transformround robinThis paper presents the first worldwide inter-laboratory comparison of small-angle X-ray scattering (SAXS) for nanoparticle sizing. The measurands in this comparison are the mean particle radius, the width of the size distribution and the particle concentration. The investigated sample consists of dispersed silver nanoparticles, surrounded by a stabilizing polymeric shell of poly(acrylic acid). The silver cores dominate the X-ray scattering pattern, leading to the determination of their radius size distribution using (i) the generalized indirect Fourier transformation method, (ii) classical model fitting using SASfit and (iii) a Monte Carlo fitting approach using McSAS. The application of these three methods to the collected data sets from the various laboratories produces consistent mean number- and volume-weighted core radii of Rn = 2.76 (6) nm and Rv = 3.20 (4) nm, respectively. The corresponding widths of the lognormal radius distribution of the particles were σn = 0.65 (1) nm and σv = 0.71 (1) nm. The particle concentration determined using this method was 3.0 (4) g l−1 or 4.2 (7) × 10−6 mol l−1. These results are affected slightly by the choice of data evaluation procedure, but not by the instruments: the participating laboratories at synchrotron SAXS beamlines, commercial and in-house-designed instruments were all able to provide highly consistent data. This demonstrates that SAXS is a suitable method for revealing particle size distributions in the sub-20 nm region (at minimum), out of reach for most other analytical methods.text/htmlNanoparticle size distribution quantification: results of a small-angle X-ray scattering inter-laboratory comparisontext5502017-08-18Copyright (c) 2017 Brian R. Pauw et al.Journal of Applied Crystallographyresearch papers12801288Determination of active layer morphology in all-polymer photovoltaic cells
http://scripts.iucr.org/cgi-bin/paper?ge5040
This study investigates the structure of films spin-coated from blends of the semiconducting polymers poly(3-hexylthiophene-2,5-diyl) (P3HT) and poly{2,6-[4,4-bis-(2-ethylhexyl)-4H-cyclopenta[2,1-b;3,4-b′]dithiophene]-alt-4,7(2,1,3-benzothiadiazole)} (PCPDTBT). Such blends are of potential use in all-polymer solar cells in which both the acceptor and the donor material generate excitons to contribute to the photocurrent. Prompted by threefold performance gains seen in polymer/fullerene and polymer blend solar cells upon addition of pristine graphene, devices are prepared from P3HT/PCPDTBT blends both with and without graphene. This report focuses on the morphology of the active layer since this is of critical importance in determining performance. Small-angle neutron scattering (SANS) is utilized to study this polymer blend with deuterated P3HT to provide contrast and permit the investigation of buried structure in neat and graphene-doped films. SANS reveals the presence of P3HT crystallites dispersed in an amorphous blend matrix of P3HT and PCPDTBT. The crystallites are approximately disc shaped and do not show any evidence of higher-order structure or aggregation. While the structure of the films does not change with the addition of graphene, there is a perceptible effect on the electronic properties and energy conversion efficiency in solar cells made from such films. Determination of the active layer morphology yields crucial insight into structure–property relationships in organic photovoltaic devices.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Mulderig, A.J.Jin, Y.Yu, F.Keum, J.Hong, K.Browning, J.F.Beaucage, G.Smith, G.S.Kuppa, V.K.2017-08-18doi:10.1107/S1600576717010457International Union of CrystallographySmall-angle scattering is used to reveal the buried nanostructure and to uncover structure–property relationships in all-polymer photovoltaics.ENorganic photovoltaicssmall-angle scatteringgraphenemorphologyThis study investigates the structure of films spin-coated from blends of the semiconducting polymers poly(3-hexylthiophene-2,5-diyl) (P3HT) and poly{2,6-[4,4-bis-(2-ethylhexyl)-4H-cyclopenta[2,1-b;3,4-b′]dithiophene]-alt-4,7(2,1,3-benzothiadiazole)} (PCPDTBT). Such blends are of potential use in all-polymer solar cells in which both the acceptor and the donor material generate excitons to contribute to the photocurrent. Prompted by threefold performance gains seen in polymer/fullerene and polymer blend solar cells upon addition of pristine graphene, devices are prepared from P3HT/PCPDTBT blends both with and without graphene. This report focuses on the morphology of the active layer since this is of critical importance in determining performance. Small-angle neutron scattering (SANS) is utilized to study this polymer blend with deuterated P3HT to provide contrast and permit the investigation of buried structure in neat and graphene-doped films. SANS reveals the presence of P3HT crystallites dispersed in an amorphous blend matrix of P3HT and PCPDTBT. The crystallites are approximately disc shaped and do not show any evidence of higher-order structure or aggregation. While the structure of the films does not change with the addition of graphene, there is a perceptible effect on the electronic properties and energy conversion efficiency in solar cells made from such films. Determination of the active layer morphology yields crucial insight into structure–property relationships in organic photovoltaic devices.text/htmlDetermination of active layer morphology in all-polymer photovoltaic cellstext5502017-08-18Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers12891298A tool for automatic recognition of [110] tilt grain boundaries in zincblende-type crystals
http://scripts.iucr.org/cgi-bin/paper?rg5134
The local atomic structure of [110] tilt grain boundaries (GBs) formed in ∼100 nm-sized GaAs nanocrystals, which crystallize in the non-centrosymmetric zincblende-type structure with face-centred cubic lattice symmetry, was imaged and analysed by means of high-resolution high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). The nanocrystals were grown by metal–organic vapour phase epitaxy on top of (001) Si nanotips embedded in an oxide matrix. This paper introduces an automatic analysis method and corresponding processing tool for the identification of the GBs. The method comprises (i) extraction of crystallographic parameters, i.e. misorientation angles and transformation matrices for the different crystal parts (grains/twins) observed by HAADF-STEM, and (ii) determination of their common plane(s) by modelling all possible intersections of the corresponding three-dimensional reciprocal lattices. The structural unit model is also used to characterize the GB structures and to validate the data obtained by the developed algorithm.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Kozak, R.Kurdzesau, F.Prieto, I.Skibitzki, O.Schroeder, T.Arroyo Rojas Dasilva, Y.Erni, R.von Känel, H.Rossell, M.D.2017-08-18doi:10.1107/S1600576717010858International Union of CrystallographyAn automated analysis approach for recognition of grain boundaries in face-centred cubic based zincblende materials from high-resolution high-angle annular dark-field scanning transmission electron microscopy images is described and its performance is tested.ENgrain/twin boundarytransformation matricesscanning transmission electron microscopyGaAsface-centred cubic zincblende nanomaterialsThe local atomic structure of [110] tilt grain boundaries (GBs) formed in ∼100 nm-sized GaAs nanocrystals, which crystallize in the non-centrosymmetric zincblende-type structure with face-centred cubic lattice symmetry, was imaged and analysed by means of high-resolution high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). The nanocrystals were grown by metal–organic vapour phase epitaxy on top of (001) Si nanotips embedded in an oxide matrix. This paper introduces an automatic analysis method and corresponding processing tool for the identification of the GBs. The method comprises (i) extraction of crystallographic parameters, i.e. misorientation angles and transformation matrices for the different crystal parts (grains/twins) observed by HAADF-STEM, and (ii) determination of their common plane(s) by modelling all possible intersections of the corresponding three-dimensional reciprocal lattices. The structural unit model is also used to characterize the GB structures and to validate the data obtained by the developed algorithm.text/htmlA tool for automatic recognition of [110] tilt grain boundaries in zincblende-type crystalstext5502017-08-18Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers12991306Expected values and variances of Bragg peak intensities measured in a nanocrystalline powder diffraction experiment
http://scripts.iucr.org/cgi-bin/paper?ks5557
A rigorous study of sampling and intensity statistics applicable for a powder diffraction experiment as a function of crystallite size is presented. This analysis yields approximate equations for the expected value, variance and standard deviations for both the number of diffracting grains and the corresponding diffracted intensity for a given Bragg peak. The classical formalism published in 1948 by Alexander, Klug & Kummer [J. Appl. Phys. (1948), 19, 742–753] appears as a special case, limited to large crystallite sizes, in the present analysis. It is observed that both the Lorentz probability expression and the statistics equations used in the classical formalism are inapplicable for nanocrystalline powder samples.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Öztürk, H.Noyan, I.C.2017-08-24doi:10.1107/S1600576717010494International Union of CrystallographyA rigorous analysis of sampling and intensity statistics for a powder diffraction experiment over a range of nanocrystallite sizes is presented.ENX-ray diffractionnanocrystalspowder diffractionsampling and intensity statisticsLorentz factorA rigorous study of sampling and intensity statistics applicable for a powder diffraction experiment as a function of crystallite size is presented. This analysis yields approximate equations for the expected value, variance and standard deviations for both the number of diffracting grains and the corresponding diffracted intensity for a given Bragg peak. The classical formalism published in 1948 by Alexander, Klug & Kummer [J. Appl. Phys. (1948), 19, 742–753] appears as a special case, limited to large crystallite sizes, in the present analysis. It is observed that both the Lorentz probability expression and the statistics equations used in the classical formalism are inapplicable for nanocrystalline powder samples.text/htmlExpected values and variances of Bragg peak intensities measured in a nanocrystalline powder diffraction experimenttext5502017-08-24Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers13071322An indexing algorithm independent of peak position extraction for X-ray powder diffraction patterns
http://scripts.iucr.org/cgi-bin/paper?to5164
Lattice parameter determination from X-ray powder diffraction patterns, called indexing, invariably requires the extraction of peak positions which are then used by indexing algorithms that are peak position dependent. The success of these algorithms depends on the accuracy of the extracted peak positions. Peak positions that do not overlap significantly with nearby peaks can be readily determined with great accuracy. However, in heavily overlapped regions it is difficult to determine the number of peaks and even more difficult to determine the peak positions accurately. This paper describes a new indexing algorithm, Lp-Search, that is implemented in the computer program TOPAS Version 7 (Bruker AXS, Karlsruhe, Germany). Lp-Search does not require peak position extraction nor does it require knowledge of the number of peaks present. Lp-Search combines Monte Carlo searches of lattice parameter space with a Pawley refinement used at the end of each search. Critical to the success of the Monte Carlo search is a new figure of merit function which allows the parameter space to be searched efficiently. Lp-Search has proved to be effective for patterns with heavily overlapped peaks; monoclinic to cubic lattices are successfully indexed in a matter of seconds and triclinic lattices within a minute or two. Diffraction patterns spanning a limited range, such that 30–40 peaks of the highest d spacing peaks are omitted, can be successfully indexed; this demonstrates the robust nature of Lp-Search.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Coelho, A.A.2017-08-24doi:10.1107/S1600576717011359International Union of CrystallographyLp-Search is an X-ray powder diffraction algorithm that is independent of peak position extraction and instead directly uses the observed data. It requires limited input parameters and should be useful for indexing problems where peak intensity extraction is difficult owing to peak overlap.ENindexingalgorithmsX-ray diffractionPawley refinementfundamental parametersLp-SearchTOPAS softwareLattice parameter determination from X-ray powder diffraction patterns, called indexing, invariably requires the extraction of peak positions which are then used by indexing algorithms that are peak position dependent. The success of these algorithms depends on the accuracy of the extracted peak positions. Peak positions that do not overlap significantly with nearby peaks can be readily determined with great accuracy. However, in heavily overlapped regions it is difficult to determine the number of peaks and even more difficult to determine the peak positions accurately. This paper describes a new indexing algorithm, Lp-Search, that is implemented in the computer program TOPAS Version 7 (Bruker AXS, Karlsruhe, Germany). Lp-Search does not require peak position extraction nor does it require knowledge of the number of peaks present. Lp-Search combines Monte Carlo searches of lattice parameter space with a Pawley refinement used at the end of each search. Critical to the success of the Monte Carlo search is a new figure of merit function which allows the parameter space to be searched efficiently. Lp-Search has proved to be effective for patterns with heavily overlapped peaks; monoclinic to cubic lattices are successfully indexed in a matter of seconds and triclinic lattices within a minute or two. Diffraction patterns spanning a limited range, such that 30–40 peaks of the highest d spacing peaks are omitted, can be successfully indexed; this demonstrates the robust nature of Lp-Search.text/htmlAn indexing algorithm independent of peak position extraction for X-ray powder diffraction patternstext5502017-08-24Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers13231330A capillary specimen aberration for describing X-ray powder diffraction line profiles for convergent, divergent and parallel beam geometries
http://scripts.iucr.org/cgi-bin/paper?te5024
X-ray powder diffraction patterns of cylindrical capillary specimens have substantially different peak positions, shapes and intensities relative to patterns from flat specimens. These aberrations vary in a complex manner with diffraction angle and instrument geometry. This paper describes a fast numerical procedure that accurately describes the capillary aberration in the equatorial plane for convergent focusing, divergent and parallel beam instrument geometries. Axial divergence effects are ignored and only a cross section of the capillary, a disc, is considered; it is assumed that axial divergence effects can be described using an additional correction that is independent of the disc correction. Significantly, the present implementation uses the TOPAS-Academic aberration approximation technique of averaging nearby aberrations in 2θ space to approximate in-between aberrations, which results in no more than ∼30 disc aberrations calculated over the entire 2θ range, even when the diffraction pattern comprises thousands of peaks. Finally, the disc aberration is convoluted with the emission profile and other instrument and specimen aberrations in a Rietveld refinement sense, allowing for refinement on the specimen's absorption coefficient and capillary diameter, as well as the instrument focal length. Large differences between refined and expected values give insight into instrument alignment.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Coelho, A.A.Rowles, M.R.2017-08-24doi:10.1107/S160057671701130XInternational Union of CrystallographyA description of peak shapes, peak intensities and peak shifts from a capillary specimen has been developed for use in X-ray powder diffraction from a fundamental parameters perspective. The capillary diameter, specimen linear absorption coefficients and focal length of the X-ray beam can be refined in a Rietveld refinement sense.ENcylindrical capillary specimensX-ray diffractionRietveld refinementfundamental parametersTOPAS-AcademicX-ray powder diffraction patterns of cylindrical capillary specimens have substantially different peak positions, shapes and intensities relative to patterns from flat specimens. These aberrations vary in a complex manner with diffraction angle and instrument geometry. This paper describes a fast numerical procedure that accurately describes the capillary aberration in the equatorial plane for convergent focusing, divergent and parallel beam instrument geometries. Axial divergence effects are ignored and only a cross section of the capillary, a disc, is considered; it is assumed that axial divergence effects can be described using an additional correction that is independent of the disc correction. Significantly, the present implementation uses the TOPAS-Academic aberration approximation technique of averaging nearby aberrations in 2θ space to approximate in-between aberrations, which results in no more than ∼30 disc aberrations calculated over the entire 2θ range, even when the diffraction pattern comprises thousands of peaks. Finally, the disc aberration is convoluted with the emission profile and other instrument and specimen aberrations in a Rietveld refinement sense, allowing for refinement on the specimen's absorption coefficient and capillary diameter, as well as the instrument focal length. Large differences between refined and expected values give insight into instrument alignment.text/htmlA capillary specimen aberration for describing X-ray powder diffraction line profiles for convergent, divergent and parallel beam geometriestext5502017-08-24Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers13311340Effect of the weather conditions during solution preparation on lysozyme crystallization
http://scripts.iucr.org/cgi-bin/paper?ap5011
Protein crystallization is a delicate process that is always sensitive to environmental factors. When the environmental factors are not well controlled or not controlled at all, identical crystallization droplets from the same mother liquid may yield different crystallization results. One environmental factor, the weather conditions during crystallization solution preparation, is not usually considered as a parameter for protein crystallization. In this paper, it is shown that the weather parameters during preparation of the crystallization experiment, including the ambient temperature, humidity, pressure and particulate matter in the air, can all affect the reproducibility of lysozyme crystallization. An identical lysozyme crystallization experiment was repeated for an entire year, and the weather conditions when each crystallization experiment was set up were recorded along with the crystallization results. Among the parameters recorded, the humidity during the experiment setup showed the strongest effect on lysozyme crystallization. On the basis of these results, it is suggested that the weather conditions during crystallization solution preparation should be considered as a potential factor that can influence protein crystallization.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Cheng, Q.-D.Chen, R.-Q.He, J.Li, D.-W.Yang, F.Liu, Y.-M.Lu, Q.-Q.Dong, C.Yin, D.-C.2017-09-05doi:10.1107/S1600576717011086International Union of CrystallographyThe weather parameters during crystallization solution preparation, including the ambient temperature, humidity, pressure and particulate matter in the air, can all affect protein crystallization. Among the parameters investigated in this study, humidity showed the strongest effect on lysozyme crystallization. The results suggest that the weather conditions during the preparation of a crystallization experiment should be considered as a potential factor that can influence protein crystallization.ENprotein crystallizationweather parameters during solution preparationcrystallization success ratecrystal optical perfectioncrystal sizeProtein crystallization is a delicate process that is always sensitive to environmental factors. When the environmental factors are not well controlled or not controlled at all, identical crystallization droplets from the same mother liquid may yield different crystallization results. One environmental factor, the weather conditions during crystallization solution preparation, is not usually considered as a parameter for protein crystallization. In this paper, it is shown that the weather parameters during preparation of the crystallization experiment, including the ambient temperature, humidity, pressure and particulate matter in the air, can all affect the reproducibility of lysozyme crystallization. An identical lysozyme crystallization experiment was repeated for an entire year, and the weather conditions when each crystallization experiment was set up were recorded along with the crystallization results. Among the parameters recorded, the humidity during the experiment setup showed the strongest effect on lysozyme crystallization. On the basis of these results, it is suggested that the weather conditions during crystallization solution preparation should be considered as a potential factor that can influence protein crystallization.text/htmlEffect of the weather conditions during solution preparation on lysozyme crystallizationtext5502017-09-05Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers13411351Berkeley Screen: a set of 96 solutions for general macromolecular crystallization
http://scripts.iucr.org/cgi-bin/paper?ei5025
Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.Copyright (c) 2017 Jose H. Pereira et al.urn:issn:1600-5767Pereira, J.H.McAndrew, R.P.Tomaleri, G.P.Adams, P.D.2017-09-05doi:10.1107/S1600576717011347International Union of CrystallographyThe Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.ENcrystallization screenscrystal packingions and bufferscrystal growthstructural biologyUsing statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.text/htmlBerkeley Screen: a set of 96 solutions for general macromolecular crystallizationtext5502017-09-05Copyright (c) 2017 Jose H. Pereira et al.Journal of Applied Crystallographyresearch papers13521358Spatially resolved texture analysis of Napoleonic War era copper bolts
http://scripts.iucr.org/cgi-bin/paper?aj5289
The spatial resolution achievable by a time-of-flight neutron strain scanner has been harnessed using a new data analysis methodology (NyRTex) to determine, nondestructively, the spatial variation of crystallographic texture in objects of cultural heritage. Previous studies on the crystallographic texture at the centre of three Napoleonic War era copper bolts, which demonstrated the value of this technique in differentiating between the different production processes of the different types of bolts, were extended to four copper bolts from the wrecks of HMS Impregnable (completed 1786), HMS Amethyst (1799), HMS Pomone (1805) and HMS Maeander (1840) along with a cylindrical `segment' of a further incomplete bolt from HMS Pomone. These included bolts with works stamps, allowing comparison with documentary accounts of the manufacturing processes used, and the results demonstrated unequivocally that bolts with a `Westwood and Collins' patent stamp were made using the Collins rather than the Westwood process. In some bolts there was a pronounced variation in texture across the cross section. In some cases this is consistent with what is known of the types of hot and cold working used, but the results from the latest study might also suggest that, even in the mature phase of this technology, some hand finishing was sometimes necessary. This examination of bolts from a wider range of dates is an important step in increasing our understanding of the introduction and evolution of copper fastenings in Royal Navy warships.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Malamud, F.Northover, S.James, J.Northover, P.Nneji, S.Kelleher, J.2017-09-05doi:10.1107/S1600576717011761International Union of CrystallographyA spatially resolved texture analysis investigation of Napoleonic War era copper bolts from four identified wrecks, HMS Impregnable (completed 1786), HMS Amethyst (1799), HMS Pomone (1805) and HMS Meander (1840), is presented.ENcopper boltstextureneutron diffractionThe spatial resolution achievable by a time-of-flight neutron strain scanner has been harnessed using a new data analysis methodology (NyRTex) to determine, nondestructively, the spatial variation of crystallographic texture in objects of cultural heritage. Previous studies on the crystallographic texture at the centre of three Napoleonic War era copper bolts, which demonstrated the value of this technique in differentiating between the different production processes of the different types of bolts, were extended to four copper bolts from the wrecks of HMS Impregnable (completed 1786), HMS Amethyst (1799), HMS Pomone (1805) and HMS Maeander (1840) along with a cylindrical `segment' of a further incomplete bolt from HMS Pomone. These included bolts with works stamps, allowing comparison with documentary accounts of the manufacturing processes used, and the results demonstrated unequivocally that bolts with a `Westwood and Collins' patent stamp were made using the Collins rather than the Westwood process. In some bolts there was a pronounced variation in texture across the cross section. In some cases this is consistent with what is known of the types of hot and cold working used, but the results from the latest study might also suggest that, even in the mature phase of this technology, some hand finishing was sometimes necessary. This examination of bolts from a wider range of dates is an important step in increasing our understanding of the introduction and evolution of copper fastenings in Royal Navy warships.text/htmlSpatially resolved texture analysis of Napoleonic War era copper boltstext5502017-09-05Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers13591375On the onset of strain relaxation in the Al0.45Ga0.55As/InxGa1−xAs active region in quantum cascade laser structures
http://scripts.iucr.org/cgi-bin/paper?po5095
The Al0.45Ga0.55As/InxGa1−xAs active regions in quantum cascade laser structures grown on (001) GaAs substrates were investigated using the high-resolution X-ray diffraction method. The onset of the strain relaxation process has been studied. Reciprocal-space mapping showed that diffuse scattering is visible in the early stage of relaxation for the structure with x = 2.64% in the InxGa1−xAs layers. It has been proved that the diffuse scattering is the result of misfit dislocations generated by partial relaxation of the structures. The integration of the diffuse scattering has enabled determination of the dislocation density.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Sankowska, I.Gutowski, P.Jasik, A.Czuba, K.Dabrowski, J.Bugajski, M.2017-09-14doi:10.1107/S1600576717011815International Union of CrystallographyThe onset of the strain relaxation process has been studied by examination of the diffuse scattering observed on symmetrical reciprocal-space maps. It is shown that the size and shape of the diffuse scattering are closely related to the density of dislocations.ENsuperlatticesdislocation densitydiffuse scatteringrelaxation mechanismsThe Al0.45Ga0.55As/InxGa1−xAs active regions in quantum cascade laser structures grown on (001) GaAs substrates were investigated using the high-resolution X-ray diffraction method. The onset of the strain relaxation process has been studied. Reciprocal-space mapping showed that diffuse scattering is visible in the early stage of relaxation for the structure with x = 2.64% in the InxGa1−xAs layers. It has been proved that the diffuse scattering is the result of misfit dislocations generated by partial relaxation of the structures. The integration of the diffuse scattering has enabled determination of the dislocation density.text/htmlOn the onset of strain relaxation in the Al0.45Ga0.55As/InxGa1−xAs active region in quantum cascade laser structurestext5502017-09-14Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers13761381Calibrating SANS data for instrument geometry and pixel sensitivity effects: access to an extended Q range
http://scripts.iucr.org/cgi-bin/paper?ks5569
An improved data-reduction procedure is proposed and demonstrated for small-angle neutron scattering (SANS) measurements. Its main feature is the correction of geometry- and wavelength-dependent intensity variations on the detector in a separate step from the different pixel sensitivities: the geometric and wavelength effects can be corrected analytically, while pixel sensitivities have to be calibrated to a reference measurement. The geometric effects are treated for position-sensitive 3He proportional counter tubes, where they are anisotropic owing to the cylindrical geometry of the gas tubes. For the calibration of pixel sensitivities, a procedure is developed that is valid for isotropic and anisotropic signals. The proposed procedure can save a significant amount of beamtime which has hitherto been used for calibration measurements.Copyright (c) 2017 Karge, Gilles and Buschurn:issn:1600-5767Karge, L.Gilles, R.Busch, S.2017-09-14doi:10.1107/S1600576717011463International Union of CrystallographyA calibration procedure for small-angle neutron scattering (SANS) data is presented, where geometric effects are treated analytically and voxel sensitivities are calibrated with measurements of an arbitrary scatterer. This allows correction of the measured intensities with a single measurement, without the need to measure an isotropic scatterer at all used instrumental settings.ENsmall-angle neutron scatteringdata reductioncalibrationcorrectionsAn improved data-reduction procedure is proposed and demonstrated for small-angle neutron scattering (SANS) measurements. Its main feature is the correction of geometry- and wavelength-dependent intensity variations on the detector in a separate step from the different pixel sensitivities: the geometric and wavelength effects can be corrected analytically, while pixel sensitivities have to be calibrated to a reference measurement. The geometric effects are treated for position-sensitive 3He proportional counter tubes, where they are anisotropic owing to the cylindrical geometry of the gas tubes. For the calibration of pixel sensitivities, a procedure is developed that is valid for isotropic and anisotropic signals. The proposed procedure can save a significant amount of beamtime which has hitherto been used for calibration measurements.text/htmlCalibrating SANS data for instrument geometry and pixel sensitivity effects: access to an extended Q rangetext5502017-09-14Copyright (c) 2017 Karge, Gilles and BuschJournal of Applied Crystallographyresearch papers13821394Transformation cycle between the spherically symmetric correlation function, projected correlation function and differential cross section as implemented in SASfit
http://scripts.iucr.org/cgi-bin/paper?ge5035
Spin-echo-based small-angle neutron scattering techniques like spin-echo SANS (SESANS) or spin-echo modulated SANS (SEMSANS) as well as dark-field (DF) imaging are directly sensitive to \tilde{G}(\delta), which is the projection of the scattering length density autocorrelation function \tilde{\gamma}(r). Here, a simplified transformation cycle relating the spherically symmetric correlation function \tilde{\gamma}(r), the projected correlation function \tilde{G}(\delta) and the macroscopic small-angle scattering cross section dΣ/dΩ is introduced. The suggested changes to the cycle make it easier to include size distribution on an absolute scale if the data from the different techniques are fitted simultaneously. As up to now only very few analytical expressions for the projected correlation function are known, a numerical transformation of known scattering functions into the projected correlation function in the SASfit software package is supplied. Furthermore, a new analytical expression for the projected correlation function for polymers that can be described by the generalized Gaussian coil model is provided. For this polymer model, the Hankel transform used to calculate \tilde{G}(0) from the SANS signal is divergent for a certain parameter range describing a polymer in a good solvent and finite in the case of a poor solvent. It is therefore a suitable example of how the experimentally available q range can strongly influence the obtained results.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Kohlbrecher, J.Studer, A.2017-09-14doi:10.1107/S1600576717011979International Union of CrystallographyThe transformation cycle between the spherically symmetric correlation function, projected correlation function and differential cross section [\tilde{\gamma}(r), \tilde{G}(\delta) and I(q)] as implemented in SASfit is described.ENspin-echo small-angle neutron scatteringsmall-angle neutron scatteringdata analysisSpin-echo-based small-angle neutron scattering techniques like spin-echo SANS (SESANS) or spin-echo modulated SANS (SEMSANS) as well as dark-field (DF) imaging are directly sensitive to \tilde{G}(\delta), which is the projection of the scattering length density autocorrelation function \tilde{\gamma}(r). Here, a simplified transformation cycle relating the spherically symmetric correlation function \tilde{\gamma}(r), the projected correlation function \tilde{G}(\delta) and the macroscopic small-angle scattering cross section dΣ/dΩ is introduced. The suggested changes to the cycle make it easier to include size distribution on an absolute scale if the data from the different techniques are fitted simultaneously. As up to now only very few analytical expressions for the projected correlation function are known, a numerical transformation of known scattering functions into the projected correlation function in the SASfit software package is supplied. Furthermore, a new analytical expression for the projected correlation function for polymers that can be described by the generalized Gaussian coil model is provided. For this polymer model, the Hankel transform used to calculate \tilde{G}(0) from the SANS signal is divergent for a certain parameter range describing a polymer in a good solvent and finite in the case of a poor solvent. It is therefore a suitable example of how the experimentally available q range can strongly influence the obtained results.text/htmlTransformation cycle between the spherically symmetric correlation function, projected correlation function and differential cross section as implemented in SASfittext5502017-09-14Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers13951403Quantifying adsorption-induced deformation of nanoporous materials on different length scales
http://scripts.iucr.org/cgi-bin/paper?vg5076
A new in situ setup combining small-angle neutron scattering (SANS) and dilatometry was used to measure water-adsorption-induced deformation of a monolithic silica sample with hierarchical porosity. The sample exhibits a disordered framework consisting of macropores and struts containing two-dimensional hexagonally ordered cylindrical mesopores. The use of an H2O/D2O water mixture with zero scattering length density as an adsorptive allows a quantitative determination of the pore lattice strain from the shift of the corresponding diffraction peak. This radial strut deformation is compared with the simultaneously measured macroscopic length change of the sample with dilatometry, and differences between the two quantities are discussed on the basis of the deformation mechanisms effective at the different length scales. It is demonstrated that the SANS data also provide a facile way to quantitatively determine the adsorption isotherm of the material by evaluating the incoherent scattering contribution of H2O at large scattering vectors.Copyright (c) 2017 Roland Morak et al.urn:issn:1600-5767Morak, R.Braxmeier, S.Ludescher, L.Putz, F.Busch, S.Hüsing, N.Reichenauer, G.Paris, O.2017-09-14doi:10.1107/S1600576717012274International Union of CrystallographySimultaneous small-angle neutron scattering and dilatometry reveal water-adsorption-induced deformation of silica materials with hierarchical porosity along with their adsorption isotherm.ENmesoporous materialssmall-angle neutron scatteringdilatometryadsorption-induced deformationadsorption isothermsA new in situ setup combining small-angle neutron scattering (SANS) and dilatometry was used to measure water-adsorption-induced deformation of a monolithic silica sample with hierarchical porosity. The sample exhibits a disordered framework consisting of macropores and struts containing two-dimensional hexagonally ordered cylindrical mesopores. The use of an H2O/D2O water mixture with zero scattering length density as an adsorptive allows a quantitative determination of the pore lattice strain from the shift of the corresponding diffraction peak. This radial strut deformation is compared with the simultaneously measured macroscopic length change of the sample with dilatometry, and differences between the two quantities are discussed on the basis of the deformation mechanisms effective at the different length scales. It is demonstrated that the SANS data also provide a facile way to quantitatively determine the adsorption isotherm of the material by evaluating the incoherent scattering contribution of H2O at large scattering vectors.text/htmlQuantifying adsorption-induced deformation of nanoporous materials on different length scalestext5502017-09-14Copyright (c) 2017 Roland Morak et al.Journal of Applied Crystallographyresearch papers14041410Improved performance of crystal structure solution from powder diffraction data through parameter tuning of a simulated annealing algorithm
http://scripts.iucr.org/cgi-bin/paper?po5104
Significant gains in the performance of the simulated annealing algorithm in the DASH software package have been realized by using the irace automatic configuration tool to optimize the values of three key simulated annealing parameters. Specifically, the success rate in finding the global minimum in intensity χ2 space is improved by up to an order of magnitude. The general applicability of these revised simulated annealing parameters is demonstrated using the crystal structure determinations of over 100 powder diffraction datasets.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Kabova, E.A.Cole, J.C.Korb, O.López-Ibáñez, M.Williams, A.C.Shankland, K.2017-09-25doi:10.1107/S1600576717012602International Union of CrystallographySignificant gains in the performance of the global optimization algorithm in the DASH software package have been realized using the irace automatic configuration tool and are demonstrated using over 100 powder diffraction datasets.ENcrystal structure determinationpowder diffractionsimulated annealingparameter tuningSignificant gains in the performance of the simulated annealing algorithm in the DASH software package have been realized by using the irace automatic configuration tool to optimize the values of three key simulated annealing parameters. Specifically, the success rate in finding the global minimum in intensity χ2 space is improved by up to an order of magnitude. The general applicability of these revised simulated annealing parameters is demonstrated using the crystal structure determinations of over 100 powder diffraction datasets.text/htmlImproved performance of crystal structure solution from powder diffraction data through parameter tuning of a simulated annealing algorithmtext5502017-09-25Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers14111420Improved crystal structure solution from powder diffraction data by the use of conformational information
http://scripts.iucr.org/cgi-bin/paper?po5105
The effect of introducing conformational information to the DASH implementation of crystal structure determination from powder diffraction data is investigated using 51 crystal structures, with the aim of allowing increasingly complex crystal structures to be solved more easily. The findings confirm that conformational information derived from the Cambridge Structural Database is indeed of value, considerably increasing the chances of obtaining a successful structure determination. Its routine use is therefore encouraged.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Kabova, E.A.Cole, J.C.Korb, O.Williams, A.C.Shankland, K.2017-09-25doi:10.1107/S1600576717012596International Union of CrystallographySignificant gains in the performance of the DASH software package have been realized using conformational information derived from the Cambridge Structural Database and are demonstrated using 51 powder diffraction data sets.ENcrystal structure determinationpowder diffractionsimulated annealingconformational informationcrystal structure databaseThe effect of introducing conformational information to the DASH implementation of crystal structure determination from powder diffraction data is investigated using 51 crystal structures, with the aim of allowing increasingly complex crystal structures to be solved more easily. The findings confirm that conformational information derived from the Cambridge Structural Database is indeed of value, considerably increasing the chances of obtaining a successful structure determination. Its routine use is therefore encouraged.text/htmlImproved crystal structure solution from powder diffraction data by the use of conformational informationtext5502017-09-25Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers14211427Extended model for the reconstruction of periodic multilayers from extreme ultraviolet and X-ray reflectivity data
http://scripts.iucr.org/cgi-bin/paper?vh5080
An extended model for the reconstruction of multilayer nanostructures from reflectometry data in the X-ray and extreme ultraviolet ranges is proposed. In contrast to the standard model approach, where the transitional region is defined in advance as a specific function, the transition layer is sought as a linear combination of several functions at once in the extended model. This allows one to describe a much wider class of multilayer structures with different dominant physical mechanisms for the formation of transition regions. The extended model occupies an intermediate position between the classical model approach and the so-called model-free methods. The efficiency of the described method is illustrated in detail in numerical simulations and in a real experiment on the annealing of a multilayer Mo/Be mirror.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Svechnikov, M.Pariev, D.Nechay, A.Salashchenko, N.Chkhalo, N.Vainer, Y.Gaman, D.2017-09-25doi:10.1107/S1600576717012286International Union of CrystallographyAn extended model for reconstruction of periodic multilayers from grazing-incidence X-ray and normal-incidence extreme ultraviolet reflectivity data is proposed; simulated and experimental data fits are presented.ENX-ray reflectometryinverse problemmodel structural reconstructionmultilayersAn extended model for the reconstruction of multilayer nanostructures from reflectometry data in the X-ray and extreme ultraviolet ranges is proposed. In contrast to the standard model approach, where the transitional region is defined in advance as a specific function, the transition layer is sought as a linear combination of several functions at once in the extended model. This allows one to describe a much wider class of multilayer structures with different dominant physical mechanisms for the formation of transition regions. The extended model occupies an intermediate position between the classical model approach and the so-called model-free methods. The efficiency of the described method is illustrated in detail in numerical simulations and in a real experiment on the annealing of a multilayer Mo/Be mirror.text/htmlExtended model for the reconstruction of periodic multilayers from extreme ultraviolet and X-ray reflectivity datatext5502017-09-25Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers14281440X-ray diffraction microscopy based on refractive optics
http://scripts.iucr.org/cgi-bin/paper?ks5571
A formalism is presented for dark-field X-ray microscopy using refractive optics. The new technique can produce three-dimensional maps of lattice orientation and axial strain within millimetre-sized sampling volumes and is particularly suited to in situ studies of materials at hard X-ray energies. An objective lens in the diffracted beam magnifies the image and acts as a very efficient filter in reciprocal space, enabling the imaging of individual domains of interest with a resolution of 100 nm. Analytical expressions for optical parameters such as numerical aperture, vignetting, and the resolution in both direct and reciprocal spaces are provided. It is shown that the resolution function in reciprocal space can be highly anisotropic and varies as a function of position in the field of view. Inserting a square aperture in front of the objective lens facilitates disjunct and space-filling sampling, which is key for three-dimensional reconstruction and analysis procedures based on the conservation of integrated intensity. A procedure for strain scanning is presented. Finally the formalism is validated experimentally at an X-ray energy of 17 keV.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Poulsen, H.F.Jakobsen, A.C.Simons, H.Ahl, S.R.Cook, P.K.Detlefs, C.2017-09-25doi:10.1107/S1600576717011037International Union of CrystallographyA formalism for dark-field X-ray microscopy is presented and validated. The coupled resolution function in direct and reciprocal space is derived and space-filling sampling approaches are described.ENX-ray diffraction microscopydiffraction contrast tomographystructural characterizationsynchrotron radiationdiffraction imagingA formalism is presented for dark-field X-ray microscopy using refractive optics. The new technique can produce three-dimensional maps of lattice orientation and axial strain within millimetre-sized sampling volumes and is particularly suited to in situ studies of materials at hard X-ray energies. An objective lens in the diffracted beam magnifies the image and acts as a very efficient filter in reciprocal space, enabling the imaging of individual domains of interest with a resolution of 100 nm. Analytical expressions for optical parameters such as numerical aperture, vignetting, and the resolution in both direct and reciprocal spaces are provided. It is shown that the resolution function in reciprocal space can be highly anisotropic and varies as a function of position in the field of view. Inserting a square aperture in front of the objective lens facilitates disjunct and space-filling sampling, which is key for three-dimensional reconstruction and analysis procedures based on the conservation of integrated intensity. A procedure for strain scanning is presented. Finally the formalism is validated experimentally at an X-ray energy of 17 keV.text/htmlX-ray diffraction microscopy based on refractive opticstext5502017-09-25Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers14411456Double crystallographic groups and their representations on the Bilbao Crystallographic Server
http://scripts.iucr.org/cgi-bin/paper?ks5574
A new section of databases and programs devoted to double crystallographic groups (point and space groups) has been implemented in the Bilbao Crystallographic Server (http://www.cryst.ehu.es). The double crystallographic groups are required in the study of physical systems whose Hamiltonian includes spin-dependent terms. In the symmetry analysis of such systems, instead of the irreducible representations of the space groups, it is necessary to consider the single- and double-valued irreducible representations of the double space groups. The new section includes databases of symmetry operations (DGENPOS) and of irreducible representations of the double (point and space) groups (REPRESENTATIONS DPG and REPRESENTATIONS DSG). The tool DCOMPREL provides compatibility relations between the irreducible representations of double space groups at different k vectors of the Brillouin zone when there is a group–subgroup relation between the corresponding little groups. The program DSITESYM implements the so-called site-symmetry approach, which establishes symmetry relations between localized and extended crystal states, using representations of the double groups. As an application of this approach, the program BANDREP calculates the band representations and the elementary band representations induced from any Wyckoff position of any of the 230 double space groups, giving information about the properties of these bands. Recently, the results of BANDREP have been extensively applied in the description of and the search for topological insulators.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Elcoro, L.Bradlyn, B.Wang, Z.Vergniory, M.G.Cano, J.Felser, C.Bernevig, B.A.Orobengoa, D.Flor, G. de laAroyo, M.I.2017-09-25doi:10.1107/S1600576717011712International Union of CrystallographyA new section of computer tools devoted to the double crystallographic groups has been implemented in the Bilbao Crystallographic Server (http://www.cryst.ehu.es). The section includes databases of symmetry operations and irreducible representations of the double point and space groups and programs that compute the compatibility relations, generate relevant information related to the site-symmetry approach, and calculate band representations and elementary band representations induced from any Wyckoff position of any double space group.ENdouble crystallographic groupssingle-valued and double-valued irreducible representationsband representationsBilbao Crystallographic Servercomputer programsA new section of databases and programs devoted to double crystallographic groups (point and space groups) has been implemented in the Bilbao Crystallographic Server (http://www.cryst.ehu.es). The double crystallographic groups are required in the study of physical systems whose Hamiltonian includes spin-dependent terms. In the symmetry analysis of such systems, instead of the irreducible representations of the space groups, it is necessary to consider the single- and double-valued irreducible representations of the double space groups. The new section includes databases of symmetry operations (DGENPOS) and of irreducible representations of the double (point and space) groups (REPRESENTATIONS DPG and REPRESENTATIONS DSG). The tool DCOMPREL provides compatibility relations between the irreducible representations of double space groups at different k vectors of the Brillouin zone when there is a group–subgroup relation between the corresponding little groups. The program DSITESYM implements the so-called site-symmetry approach, which establishes symmetry relations between localized and extended crystal states, using representations of the double groups. As an application of this approach, the program BANDREP calculates the band representations and the elementary band representations induced from any Wyckoff position of any of the 230 double space groups, giving information about the properties of these bands. Recently, the results of BANDREP have been extensively applied in the description of and the search for topological insulators.text/htmlDouble crystallographic groups and their representations on the Bilbao Crystallographic Servertext5502017-09-25Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers14571477X-ray diffraction study on a (111)-textured palladium thin film under hydrogen loading and unloading: film structure evolution and its mechanism
http://scripts.iucr.org/cgi-bin/paper?nb5202
The incorporation of hydrogen normally results in degradation when applied to metals. In this diffraction study, however, improvement of the film structure, such as in-plane grain growth, lattice defect removal and texture enhancement, was observed in a (111)-textured palladium thin film during hydrogen loading and unloading cycles. Accordingly, diffraction stress analysis was performed to investigate the evolution mechanism. It was found that the formation of the β phase during the α-to-β phase transformation occurred at the same in-plane stress present in the α phase, and vice versa. This suggests that the cyclic α–β grain boundary motion during the transformation occurred mainly along the in-plane direction, contributing to the film structure evolution.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Harumoto, T.Suzuki, Y.Shi, J.Nakamura, Y.2017-09-28doi:10.1107/S1600576717012638International Union of CrystallographyAn X-ray diffraction study was conducted on a (111)-textured palladium thin film under cyclic hydrogen loading. The film structure evolution was observed and its mechanism investigated.ENhydrogenpalladiumdiffraction stress analysisin situ X-ray diffractionstructure evolutionThe incorporation of hydrogen normally results in degradation when applied to metals. In this diffraction study, however, improvement of the film structure, such as in-plane grain growth, lattice defect removal and texture enhancement, was observed in a (111)-textured palladium thin film during hydrogen loading and unloading cycles. Accordingly, diffraction stress analysis was performed to investigate the evolution mechanism. It was found that the formation of the β phase during the α-to-β phase transformation occurred at the same in-plane stress present in the α phase, and vice versa. This suggests that the cyclic α–β grain boundary motion during the transformation occurred mainly along the in-plane direction, contributing to the film structure evolution.text/htmlX-ray diffraction study on a (111)-textured palladium thin film under hydrogen loading and unloading: film structure evolution and its mechanismtext5502017-09-28Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers14781489A new model for the description of X-ray diffraction from mosaic crystals for ray-tracing calculations
http://scripts.iucr.org/cgi-bin/paper?aj5296
This paper presents the development of a new reflection model for describing X-ray diffraction from mosaic crystals. In contrast to the well established diffraction model of Zachariasen [Zachariasen (1994), Theory of X-ray Diffraction in Crystals. Mineola: Dover Publications], it gives additional information on the spatial reflection behaviour and not just on the depth-integrated reflectivity of the crystal material. The new reflection model enables a concrete description of mosaic crystal performance in an arbitrary X-ray spectrometer configuration. Multiple reflections inside the crystal are described by splitting the calculation into a discrete number of reflections. Hence, the influence of each number of reflections is investigated, leading to a laterally resolved solution for the reflectivity. In addition, the model can use a mosaicity of arbitrary shape. This is important because the present work uses a Lorentzian-shaped mosaicity instead of a Gaussian one, which is usually the case in the most widely used simulation programs. A comparison between the new model and that of Zachariasen is performed, and it predicts a similar integrated reflectivity with a deviation lower than 0.7%. Further, a ray-tracing simulation with multiple reflections based on the new model is compared with a measurement, showing a deviation of lower than 5%.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Schlesiger, C.Anklamm, L.Malzer, W.Gnewkow, R.Kanngießer, B.2017-09-28doi:10.1107/S1600576717012626International Union of CrystallographyA new reflection model for X-ray diffraction from mosaic crystals has been developed with which it is possible, in contrast to Zachariasen's well established model, to describe the crystal reflectivity in a spatially resolved manner. Introduced in a ray-tracing simulation, the simulations show very good agreement with measurements, because multiple reflections and their spatial effects are included.ENmosaic crystalsdiffraction modelX-ray diffractionhighly annealed pyrolytic graphiteHAPGThis paper presents the development of a new reflection model for describing X-ray diffraction from mosaic crystals. In contrast to the well established diffraction model of Zachariasen [Zachariasen (1994), Theory of X-ray Diffraction in Crystals. Mineola: Dover Publications], it gives additional information on the spatial reflection behaviour and not just on the depth-integrated reflectivity of the crystal material. The new reflection model enables a concrete description of mosaic crystal performance in an arbitrary X-ray spectrometer configuration. Multiple reflections inside the crystal are described by splitting the calculation into a discrete number of reflections. Hence, the influence of each number of reflections is investigated, leading to a laterally resolved solution for the reflectivity. In addition, the model can use a mosaicity of arbitrary shape. This is important because the present work uses a Lorentzian-shaped mosaicity instead of a Gaussian one, which is usually the case in the most widely used simulation programs. A comparison between the new model and that of Zachariasen is performed, and it predicts a similar integrated reflectivity with a deviation lower than 0.7%. Further, a ray-tracing simulation with multiple reflections based on the new model is compared with a measurement, showing a deviation of lower than 5%.text/htmlA new model for the description of X-ray diffraction from mosaic crystals for ray-tracing calculationstext5502017-09-28Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers14901497An insight into the synthesis, crystal structure, geometrical modelling of crystal morphology, Hirshfeld surface analysis and characterization of N-(4-methylbenzyl)benzamide single crystals
http://scripts.iucr.org/cgi-bin/paper?ei5022
A versatile approach for the synthesis of N-(4-methylbenzyl)benzamide, C15H15NO, using CuI as catalyst has been reported. Single crystals of the synthesized compound were grown using the slow evaporation solution technique. The crystal structure of the N-(4-methylbenzyl)benzamide crystals has been determined by single-crystal X-ray diffraction. The compound crystallizes in an orthorhombic lattice, noncentrosymmetric space group Pna21. The crystal structure is stabilized by intermolecular N—H...O hydrogen bonds and weak C—H...π interactions to form layers parallel to the a axis. A user-friendly approach based on centre of mass propagation vector theory was used to predict the crystal morphology. The framework developed here utilizes the concept of intermolecular bond strength to discern the crystal morphology. Fourier transform IR, NMR and high-resolution mass spectrometry analytical techniques were used for the identification of functional groups and confirmation of the structure of the title compound. All of the intermolecular interactions present in the crystal structure, including the C—H...π, C—H...O and N—H...O interactions, were investigated and confirmed by molecular Hirshfeld surface analysis. From linear optical spectroscopy, the transmittance, optical band gap and UV cutoff wavelength were determined. The photoluminescence emission spectrum was recorded for a grown crystal. Dielectric measurements were performed at room temperature for various frequencies. The mechanical strength of the (001) plane of the title compound was measured using the Vickers micro-hardness technique. A piezo-coefficient of 15 pC N−1 was found along the (001) plane of the title crystals. The thermal stability and melting point were also investigated. In addition, density functional theory simulations were used to calculate the optimized molecular geometry and the UV–vis spectrum, and to determine the highest occupied molecular orbital/lowest unoccupied molecular orbital energy gap. The results show that N-(4-methylbenzyl)benzamide is a potential candidate for multifunctional optical and piezoelectric crystals.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Goel, S.Yadav, H.Sinha, N.Singh, B.Bdikin, I.Rao, D.C.Gopalaiah, K.Kumar, B.2017-09-28doi:10.1107/S1600576717012316International Union of CrystallographyIntermolecular interactions in the N-(4-methylbenzyl)benzamide crystal are perfectly discerned using a Hirshfeld surface. A method to determine the crystal morphology from the propagation vector of the centre of mass of the molecular basis in the crystal system is outlined.ENN-(4-methylbenzyl)benzamidecrystal structurecrystal morphologycentre of mass propagation vectorHirshfeld surface analysisphotoluminescencepiezoelectricityA versatile approach for the synthesis of N-(4-methylbenzyl)benzamide, C15H15NO, using CuI as catalyst has been reported. Single crystals of the synthesized compound were grown using the slow evaporation solution technique. The crystal structure of the N-(4-methylbenzyl)benzamide crystals has been determined by single-crystal X-ray diffraction. The compound crystallizes in an orthorhombic lattice, noncentrosymmetric space group Pna21. The crystal structure is stabilized by intermolecular N—H...O hydrogen bonds and weak C—H...π interactions to form layers parallel to the a axis. A user-friendly approach based on centre of mass propagation vector theory was used to predict the crystal morphology. The framework developed here utilizes the concept of intermolecular bond strength to discern the crystal morphology. Fourier transform IR, NMR and high-resolution mass spectrometry analytical techniques were used for the identification of functional groups and confirmation of the structure of the title compound. All of the intermolecular interactions present in the crystal structure, including the C—H...π, C—H...O and N—H...O interactions, were investigated and confirmed by molecular Hirshfeld surface analysis. From linear optical spectroscopy, the transmittance, optical band gap and UV cutoff wavelength were determined. The photoluminescence emission spectrum was recorded for a grown crystal. Dielectric measurements were performed at room temperature for various frequencies. The mechanical strength of the (001) plane of the title compound was measured using the Vickers micro-hardness technique. A piezo-coefficient of 15 pC N−1 was found along the (001) plane of the title crystals. The thermal stability and melting point were also investigated. In addition, density functional theory simulations were used to calculate the optimized molecular geometry and the UV–vis spectrum, and to determine the highest occupied molecular orbital/lowest unoccupied molecular orbital energy gap. The results show that N-(4-methylbenzyl)benzamide is a potential candidate for multifunctional optical and piezoelectric crystals.text/htmlAn insight into the synthesis, crystal structure, geometrical modelling of crystal morphology, Hirshfeld surface analysis and characterization of N-(4-methylbenzyl)benzamide single crystalstext5502017-09-28Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers149815111524601Morphological and crystallographic anisotropy of severely deformed commercially pure aluminium by three-dimensional electron backscatter diffraction
http://scripts.iucr.org/cgi-bin/paper?ks5563
The aim of this paper is to examine the morphological and crystallographic anisotropy that develops during high-pressure torsion (HPT) processing. Commercially pure aluminium was subjected to monotonic HPT deformation at room temperature. The microstructure and texture were studied by large-area electron backscatter diffraction (EBSD) scans. Three-dimensional EBSD scans served to scrutinize the morphological anisotropy and local texture. It was observed that two distinct stages of grain fragmentation and saturation occur during processing. Grains exhibited an ellipsoidal shape rather than an equi-axed one. The major axes of the ellipsoids showed a favorable orientation at the steady-state stage: an almost 20° inclination towards the shear direction. The global texture was characterized by typical shear components of face-centered cubic metals at both stages. However, the local texture revealed a preferential fragmentation pattern in the first stage: orientations in the vicinity of ideal fibers became less heavily fragmented while non-ideal orientations broke up more severely. This phenomenon was linked with the lattice rotation required to bring an initial orientation close to a stable one. Although the texture weakened considerably in the fragmentation stage, the texture index did not further decrease in the saturation stage. Saturation of texture, grain refinement and formation of microstructure are discussed in the light of different microstructural coarsening mechanisms.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Naghdy, S.Pirgazi, H.Verleysen, P.Petrov, R.Kestens, L.2017-09-28doi:10.1107/S1600576717012754International Union of CrystallographyMorphological and crystallographic anisotropy of severely deformed commercially pure aluminium is studied by conventional and three-dimensional electron backscatter diffraction. Saturation of texture, grain refinement and the formation of microstructure are discussed in the light of different microstructural coarsening mechanisms.ENaluminiumhigh-pressure torsion (HPT)three-dimensional electron backscatter diffraction (3D-EBSD)grain fragmentationanisotropyThe aim of this paper is to examine the morphological and crystallographic anisotropy that develops during high-pressure torsion (HPT) processing. Commercially pure aluminium was subjected to monotonic HPT deformation at room temperature. The microstructure and texture were studied by large-area electron backscatter diffraction (EBSD) scans. Three-dimensional EBSD scans served to scrutinize the morphological anisotropy and local texture. It was observed that two distinct stages of grain fragmentation and saturation occur during processing. Grains exhibited an ellipsoidal shape rather than an equi-axed one. The major axes of the ellipsoids showed a favorable orientation at the steady-state stage: an almost 20° inclination towards the shear direction. The global texture was characterized by typical shear components of face-centered cubic metals at both stages. However, the local texture revealed a preferential fragmentation pattern in the first stage: orientations in the vicinity of ideal fibers became less heavily fragmented while non-ideal orientations broke up more severely. This phenomenon was linked with the lattice rotation required to bring an initial orientation close to a stable one. Although the texture weakened considerably in the fragmentation stage, the texture index did not further decrease in the saturation stage. Saturation of texture, grain refinement and formation of microstructure are discussed in the light of different microstructural coarsening mechanisms.text/htmlMorphological and crystallographic anisotropy of severely deformed commercially pure aluminium by three-dimensional electron backscatter diffractiontext5502017-09-28Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers15121523Reconstructing detailed line profiles of lamellar gratings from GISAXS patterns with a Maxwell solver
http://scripts.iucr.org/cgi-bin/paper?rg5133
Laterally periodic nanostructures have been investigated with grazing-incidence small-angle X-ray scattering (GISAXS) by using the diffraction patterns to reconstruct the surface shape. To model visible light scattering, rigorous calculations of the near and far field by numerical solution of Maxwell's equations with a finite-element method are well established. The application of this technique to X-rays is still challenging, owing to the discrepancy between the incident wavelength and the finite-element size. This drawback vanishes for GISAXS because of the small angles of incidence, the conical scattering geometry and the periodicity of the surface structures, which allows a rigorous computation of the diffraction efficiencies with sufficient numerical precision. To develop metrology tools based on GISAXS, lamellar gratings with line widths down to 55 nm were produced by state-of-the-art electron-beam lithography and then etched into silicon. The high surface sensitivity of GISAXS in conjunction with a Maxwell solver allows the detailed reconstruction of the grating line shape for thick non-homogeneous substrates as well. The reconstructed geometric line-shape models are statistically validated by applying a Markov chain Monte Carlo sampling technique which reveals that GISAXS is able to reconstruct critical parameters like the widths of the lines with sub-nanometre uncertainty.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Soltwisch, V.Fernández Herrero, A.Pflüger, M.Haase, A.Probst, J.Laubis, C.Krumrey, M.Scholze, F.2017-09-28doi:10.1107/S1600576717012742International Union of CrystallographyThe shallow incidence angles in grazing-incidence small-angle X-ray scattering (GISAXS) allow the use of a rigorous Maxwell solver in combination with the finite-element method for the reconstruction of nanometre-sized periodic surface structures.ENline profileslamellar gratingsgrazing-incidence small-angle X-ray scatteringGISAXSMaxwell solversfinite-element methodMarkov chain Monte Carlo techniquereconstructionmetrologyLaterally periodic nanostructures have been investigated with grazing-incidence small-angle X-ray scattering (GISAXS) by using the diffraction patterns to reconstruct the surface shape. To model visible light scattering, rigorous calculations of the near and far field by numerical solution of Maxwell's equations with a finite-element method are well established. The application of this technique to X-rays is still challenging, owing to the discrepancy between the incident wavelength and the finite-element size. This drawback vanishes for GISAXS because of the small angles of incidence, the conical scattering geometry and the periodicity of the surface structures, which allows a rigorous computation of the diffraction efficiencies with sufficient numerical precision. To develop metrology tools based on GISAXS, lamellar gratings with line widths down to 55 nm were produced by state-of-the-art electron-beam lithography and then etched into silicon. The high surface sensitivity of GISAXS in conjunction with a Maxwell solver allows the detailed reconstruction of the grating line shape for thick non-homogeneous substrates as well. The reconstructed geometric line-shape models are statistically validated by applying a Markov chain Monte Carlo sampling technique which reveals that GISAXS is able to reconstruct critical parameters like the widths of the lines with sub-nanometre uncertainty.text/htmlReconstructing detailed line profiles of lamellar gratings from GISAXS patterns with a Maxwell solvertext5502017-09-28Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers15241532Nanocrystallography measurements of early stage synthetic malaria pigment
http://scripts.iucr.org/cgi-bin/paper?ap5010
The recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic form of hemozoin which is a waste by-product of the malaria parasite. This analysis reveals significant differences in β-hematin data collected during SFX and synchrotron crystallography experiments. To interpret these differences two possibilities are considered: structural differences between the nanocrystal and larger crystalline forms of β-hematin, and radiation damage. Simulation studies show that structural inhomogeneity appears at present to provide a better fit to the experimental data. If confirmed, these observations will have implications for designing compounds that inhibit hemozoin formation and suggest that, for some systems at least, additional information may be gained by comparing structures obtained from nanocrystals and macroscopic crystals of the same molecule.Copyright (c) 2017 Ruben A. Dilanian et al.urn:issn:1600-5767Dilanian, R.A.Streltsov, V.Coughlan, H.D.Quiney, H.M.Martin, A.V.Klonis, N.Dogovski, C.Boutet, S.Messerschmidt, M.Williams, G.J.Williams, S.Phillips, N.W.Nugent, K.A.Tilley, L.Abbey, B.2017-09-28doi:10.1107/S1600576717012663International Union of CrystallographySerial femtosecond crystallography (SFX) at an X-ray free-electron laser enables crystllographic data to be collected from samples orders of magnitude smaller than at a synchrotron. Here SFX is used to investigate the nascent structure of β-hematin derived from nanocrystals and this is compared with the well known structure derived from macroscopic crystals of the same material.ENcrystallographyserial femtosecond nanocrystallographymalariacrystalline disorderstructural inhomogenietyThe recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic form of hemozoin which is a waste by-product of the malaria parasite. This analysis reveals significant differences in β-hematin data collected during SFX and synchrotron crystallography experiments. To interpret these differences two possibilities are considered: structural differences between the nanocrystal and larger crystalline forms of β-hematin, and radiation damage. Simulation studies show that structural inhomogeneity appears at present to provide a better fit to the experimental data. If confirmed, these observations will have implications for designing compounds that inhibit hemozoin formation and suggest that, for some systems at least, additional information may be gained by comparing structures obtained from nanocrystals and macroscopic crystals of the same molecule.text/htmlNanocrystallography measurements of early stage synthetic malaria pigmenttext5502017-09-28Copyright (c) 2017 Ruben A. Dilanian et al.Journal of Applied Crystallographyresearch papers15331540Direction indices for crystal lattices
http://scripts.iucr.org/cgi-bin/paper?gj5187
Direction indices [uvw] of rational directions in crystal lattices are commonly restricted to integer numbers. This restriction is correct only when primitive unit cells are used. In the case of centred cells, however, direction indices may take fractional values too, because the first lattice node after the origin along a direction can have fractional coordinates in a centred basis. This evidence is very often overlooked and an undue simplification of direction indices to integer values is usually adopted. Although such a simplification does not affect the identification of the direction, it is potentially a source of confusion and mistakes in crystallographic calculations. A parallel is made with the incorrect restriction of Miller indices to relatively prime integers in centred cells.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Nespolo, M.2017-08-09doi:10.1107/S1600576717010548International Union of CrystallographyThe incorrect restriction to integer values for direction indices in centred cells and the potential consequences are pointed out and corrected.ENdirection indicesMiller indicescentred cellsDirection indices [uvw] of rational directions in crystal lattices are commonly restricted to integer numbers. This restriction is correct only when primitive unit cells are used. In the case of centred cells, however, direction indices may take fractional values too, because the first lattice node after the origin along a direction can have fractional coordinates in a centred basis. This evidence is very often overlooked and an undue simplification of direction indices to integer values is usually adopted. Although such a simplification does not affect the identification of the direction, it is potentially a source of confusion and mistakes in crystallographic calculations. A parallel is made with the incorrect restriction of Miller indices to relatively prime integers in centred cells.text/htmlDirection indices for crystal latticestext5502017-08-09Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyteaching and education15411544BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis
http://scripts.iucr.org/cgi-bin/paper?ge5036
BioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software is designed for biological SAXS data and enables creation and plotting of one-dimensional scattering profiles from two-dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and advanced analysis such as calculation of inverse Fourier transforms and envelopes. It also allows easy processing of inline size-exclusion chromatography coupled SAXS data and data deconvolution using the evolving factor analysis method. It provides an alternative to closed-source programs such as Primus and ScÅtter for primary data analysis. Because it can calibrate, mask and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.Copyright (c) 2017 Jesse Bennett Hopkins et al.urn:issn:1600-5767Hopkins, J.B.Gillilan, R.E.Skou, S.2017-09-05doi:10.1107/S1600576717011438International Union of CrystallographyBioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data, including size-exclusion chromatography coupled SAXS data. The software is designed for biological data and enables creation and plotting of one-dimensional scattering profiles from two-dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and more advanced analyses such as calculation of inverse Fourier transforms.ENsmall-angle X-ray scatteringSAXSdata analysissize exclusion chromatographySEC-SAXScomputer programsBioXTAS RAWBioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software is designed for biological SAXS data and enables creation and plotting of one-dimensional scattering profiles from two-dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and advanced analysis such as calculation of inverse Fourier transforms and envelopes. It also allows easy processing of inline size-exclusion chromatography coupled SAXS data and data deconvolution using the evolving factor analysis method. It provides an alternative to closed-source programs such as Primus and ScÅtter for primary data analysis. Because it can calibrate, mask and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.text/htmlBioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysistext5502017-09-05Copyright (c) 2017 Jesse Bennett Hopkins et al.Journal of Applied Crystallographycomputer programs15451553A simple device for transferring an oriented crystal from an X-ray Laue diffractometer to a cutting machine
http://scripts.iucr.org/cgi-bin/paper?vg5073
A simple transfer device is described that enables cutting of an oriented single crystal.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Stishov, S.M.2017-08-18doi:10.1107/S1600576717010469International Union of CrystallographyA simple transfer device is described that enables cutting of an oriented single crystal.ENcrystal orientationLaue X-ray diffractionA simple transfer device is described that enables cutting of an oriented single crystal.text/htmlA simple device for transferring an oriented crystal from an X-ray Laue diffractometer to a cutting machinetext5502017-08-18Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographylaboratory notes15541555In situ laser irradiation setup for a Bruker three-circle goniometer
http://scripts.iucr.org/cgi-bin/paper?rg5138
A new design of a setup for in situ laser irradiation of single crystals during an X-ray diffraction experiment is presented. The system is designed for use with a Bruker three-circle goniometer in combination with a Helix ultra-low-temperature cryostat and consists of a laser mount and a set of three adjustable mirrors. The main advantages of the presented system include a stationary laser mount, the ability to irradiate a sample inside the Be nozzle and no impediments to the goniometer movements.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Yufit, D.S.2017-09-14doi:10.1107/S1600576717012067International Union of CrystallographyA new design of a setup for in situ laser irradiation of single crystals during an X-ray diffraction experiment is reported.ENin situ irradiationlasersthree-circle goniometersHelix low-temperature devicesA new design of a setup for in situ laser irradiation of single crystals during an X-ray diffraction experiment is presented. The system is designed for use with a Bruker three-circle goniometer in combination with a Helix ultra-low-temperature cryostat and consists of a laser mount and a set of three adjustable mirrors. The main advantages of the presented system include a stationary laser mount, the ability to irradiate a sample inside the Be nozzle and no impediments to the goniometer movements.text/htmlIn situ laser irradiation setup for a Bruker three-circle goniometertext5502017-09-14Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographylaboratory notes15561558Expanding Lorentz and spectrum corrections to large volumes of reciprocal space for single-crystal time-of-flight neutron diffraction. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?fs9119
The author list of the article by Michels-Clark et al. [J. Appl. Cryst. (2016), 49, 497–506] is amended with the addition of Michal Chodkiewicz, Thomas Weber and Hans-Beat Bürgi. The complete list of authors is Tara Michels-Clark, Andrei Savici, Vickie Lynch, Xiaoping Wang, Michal Chodkiewicz, Thomas Weber, Hans-Beat Bürgi and Christina Hoffmann.Copyright (c) 2017 Tara M. Michels-Clark et al.urn:issn:1600-5767Michels-Clark, T.M.Savici, A.T.Lynch, V.E.Wang, X.Chodkiewicz, M.Weber, T.Bürgi, H.-B.Hoffmann, C.M.2017-09-25doi:10.1107/S1600576717006781International Union of CrystallographyCorrigendum to J. Appl. Cryst. (2016), 49, 497–506: addition of co-authors.ENmodulated diffuse scatteringlocal structure modelingLorentz and spectrum correctionssingle-crystal time-of-flight neutron diffractionThe author list of the article by Michels-Clark et al. [J. Appl. Cryst. (2016), 49, 497–506] is amended with the addition of Michal Chodkiewicz, Thomas Weber and Hans-Beat Bürgi. The complete list of authors is Tara Michels-Clark, Andrei Savici, Vickie Lynch, Xiaoping Wang, Michal Chodkiewicz, Thomas Weber, Hans-Beat Bürgi and Christina Hoffmann.text/htmlExpanding Lorentz and spectrum corrections to large volumes of reciprocal space for single-crystal time-of-flight neutron diffraction. Corrigendumtext5502017-09-25Copyright (c) 2017 Tara M. Michels-Clark et al.Journal of Applied Crystallographyaddenda and errata15591559Professor G. B. Mitra (1923–2017)
http://scripts.iucr.org/cgi-bin/paper?es0430
Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Dasgupta, P.2017-09-05doi:10.1107/S1600576717012493International Union of CrystallographyObituary for G. B. Mitra.ENobituarytext/htmlProfessor G. B. Mitra (1923–2017)text5502017-09-05Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographycrystallographers15601560