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) 2018 International Union of Crystallography2017-12-14International 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 51, Part 1, 2018textweekly62002-02-01T00:00+00:001512017-12-14Copyright (c) 2018 International Union of CrystallographyJournal of Applied Crystallography1urn:issn:1600-5767med@iucr.orgDecember 20172017-12-14Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
//journals.iucr.org/j/issues/2018/01/00/isscontsbdy.html
Still imageDesign and performance of the variable-wavelength Bonse–Hart ultra-small-angle neutron scattering diffractometer KOOKABURRA at ANSTO
http://scripts.iucr.org/cgi-bin/paper?aj5304
The double-crystal ultra-small-angle neutron scattering (USANS) diffractometer KOOKABURRA at ANSTO was made available for user experiments in 2014. KOOKABURRA allows the characterization of microstructures covering length scales in the range of 0.1–10 µm. Use of the first- and second-order reflections coming off a doubly curved highly oriented mosaic pyrolytic graphite premonochromator at a fixed Bragg angle, in conjunction with two interchangeable pairs of Si(111) and Si(311) quintuple-reflection channel-cut crystals, permits operation of the instrument at two individual wavelengths, 4.74 and 2.37 Å. This unique feature among reactor-based USANS instruments allows optimal accommodation of a broad range of samples, both weakly and strongly scattering, in one sample setup. The versatility and capabilities of KOOKABURRA have already resulted in a number of research papers, clearly demonstrating that this instrument has a major impact in the field of large-scale structure determination.Copyright (c) 2018 International Union of Crystallographyurn:issn:1600-5767Rehm, C.Campo, L. deBrûlé, A.Darmann, F.Bartsch, F.Berry, A.2018-02-01doi:10.1107/S1600576717016879International Union of CrystallographyThe concept, design and performance of the variable-wavelength Bonse–Hart ultra-small-angle neutron scattering diffractometer KOOKABURRA at ANSTO are described.ENultra-small-angle neutron scatteringBonse–Hartmicrostructure characterizationKOOKABURRAThe double-crystal ultra-small-angle neutron scattering (USANS) diffractometer KOOKABURRA at ANSTO was made available for user experiments in 2014. KOOKABURRA allows the characterization of microstructures covering length scales in the range of 0.1–10 µm. Use of the first- and second-order reflections coming off a doubly curved highly oriented mosaic pyrolytic graphite premonochromator at a fixed Bragg angle, in conjunction with two interchangeable pairs of Si(111) and Si(311) quintuple-reflection channel-cut crystals, permits operation of the instrument at two individual wavelengths, 4.74 and 2.37 Å. This unique feature among reactor-based USANS instruments allows optimal accommodation of a broad range of samples, both weakly and strongly scattering, in one sample setup. The versatility and capabilities of KOOKABURRA have already resulted in a number of research papers, clearly demonstrating that this instrument has a major impact in the field of large-scale structure determination.text/htmlDesign and performance of the variable-wavelength Bonse–Hart ultra-small-angle neutron scattering diffractometer KOOKABURRA at ANSTOtext1512018-02-01Copyright (c) 2018 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Aluminium diboride-type structure in Ethiopian opal-CT revealed by fast Fourier transform
http://scripts.iucr.org/cgi-bin/paper?gj5192
Invisible on a scanning electron microscope image of the surface of an Ethiopian opal rough fracture, a periodic arrangement was detected by fast Fourier transform. Using a mask to eliminate the continuous background and keeping only the bright spots in the reciprocal space (fast Fourier transform pattern), an image reconstructed by inverse fast Fourier transform (IFFT) emphasizes a very regular bidisperse array. Taken on a vicinal plane, the image of the successive steps of the stacking allows identification of the crystallographic structure and estimation of the parameters of this aluminium diboride-type photonic crystal. In addition, another more complex IFFT image allowed confirmation of the structure and determination of the crystallographic indexing of the steps, despite image deformation due to the tilt of the vicinal plane under the electron beam.Copyright (c) 2018 International Union of Crystallographyurn:issn:1600-5767Gauthier, J.-P.Stephant, N.Rondeau, B.Cody, J.A.Fritsch, E.2018-02-01doi:10.1107/S1600576717016387International Union of CrystallographyThe structure of a natural CT opal from Ethiopia is explored with a new method, using Fourier transformation, applied to scanning electron microscope images.ENfast Fourier transformopal-CTbinary systemsbidisperse arrangementEthiopian opalvicinal planesscanning electron microscopySEMInvisible on a scanning electron microscope image of the surface of an Ethiopian opal rough fracture, a periodic arrangement was detected by fast Fourier transform. Using a mask to eliminate the continuous background and keeping only the bright spots in the reciprocal space (fast Fourier transform pattern), an image reconstructed by inverse fast Fourier transform (IFFT) emphasizes a very regular bidisperse array. Taken on a vicinal plane, the image of the successive steps of the stacking allows identification of the crystallographic structure and estimation of the parameters of this aluminium diboride-type photonic crystal. In addition, another more complex IFFT image allowed confirmation of the structure and determination of the crystallographic indexing of the steps, despite image deformation due to the tilt of the vicinal plane under the electron beam.text/htmlAluminium diboride-type structure in Ethiopian opal-CT revealed by fast Fourier transformtext1512018-02-01Copyright (c) 2018 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Inverse transformation: unleashing spatially heterogeneous dynamics with an alternative approach to XPCS data analysis
http://scripts.iucr.org/cgi-bin/paper?te5020
X-ray photon correlation spectroscopy (XPCS), an extension of dynamic light scattering (DLS) in the X-ray regime, detects temporal intensity fluctuations of coherent speckles and provides scattering-vector-dependent sample dynamics at length scales smaller than DLS. The penetrating power of X-rays enables XPCS to probe the dynamics in a broad array of materials, including polymers, glasses and metal alloys, where attempts to describe the dynamics with a simple exponential fit usually fail. In these cases, the prevailing XPCS data analysis approach employs stretched or compressed exponential decay functions (Kohlrausch functions), which implicitly assume homogeneous dynamics. This paper proposes an alternative analysis scheme based upon inverse Laplace or Gaussian transformation for elucidating heterogeneous distributions of dynamic time scales in XPCS, an approach analogous to the CONTIN algorithm widely accepted in the analysis of DLS from polydisperse and multimodal systems. Using XPCS data measured from colloidal gels, it is demonstrated that the inverse transform approach reveals hidden multimodal dynamics in materials, unleashing the full potential of XPCS.Copyright (c) 2018 International Union of Crystallographyurn:issn:1600-5767Andrews, R.N.Narayanan, S.Zhang, F.Kuzmenko, I.Ilavsky, J.2018-02-01doi:10.1107/S1600576717015795International Union of CrystallographyThis work describes an inverse transform approach for analysis of X-ray photon correlation spectroscopy (XPCS) data that reveals dynamic heterogeneity.ENX-ray photon correlation spectroscopyXPCSCONTINMULTIQinverse transform analysisheterogeneous dynamicsX-ray photon correlation spectroscopy (XPCS), an extension of dynamic light scattering (DLS) in the X-ray regime, detects temporal intensity fluctuations of coherent speckles and provides scattering-vector-dependent sample dynamics at length scales smaller than DLS. The penetrating power of X-rays enables XPCS to probe the dynamics in a broad array of materials, including polymers, glasses and metal alloys, where attempts to describe the dynamics with a simple exponential fit usually fail. In these cases, the prevailing XPCS data analysis approach employs stretched or compressed exponential decay functions (Kohlrausch functions), which implicitly assume homogeneous dynamics. This paper proposes an alternative analysis scheme based upon inverse Laplace or Gaussian transformation for elucidating heterogeneous distributions of dynamic time scales in XPCS, an approach analogous to the CONTIN algorithm widely accepted in the analysis of DLS from polydisperse and multimodal systems. Using XPCS data measured from colloidal gels, it is demonstrated that the inverse transform approach reveals hidden multimodal dynamics in materials, unleashing the full potential of XPCS.text/htmlInverse transformation: unleashing spatially heterogeneous dynamics with an alternative approach to XPCS data analysistext1512018-02-01Copyright (c) 2018 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Organizing a crystallization laboratory
http://scripts.iucr.org/cgi-bin/paper?ap5021
Managing chemical stocks and samples in any laboratory is an arduous task; in a crystallization laboratory this is particularly burdensome, given the need for many stocks to facilitate optimization of crystal hits obtained from screening experiments. Although inventory management is widespread in retail and other arenas, most small academic laboratories do not adopt formal stock management systems. Without an overarching system for handling stocks and samples, problems such as stock duplication, inappropriate stock storage and insufficient labelling are rife. Two applications have been developed in the Collaborative Crystallization Centre, the first of which manages the hundreds of stocks used for crystallization, and a second which manages protein (and other) samples stored in the 193 K freezer. Both applications are built around a simple database, with a Python front end that allows samples or stocks to be scanned in or out. Information from a decade of crystallization stock usage allows a good estimation of what chemicals are used (and in what quantities) in a crystallization laboratory.Copyright (c) 2018 International Union of Crystallographyurn:issn:1600-5767Gu, A.Marshall, B.Rosa, N.Ristic, M.Newman, J.2018-02-01doi:10.1107/S1600576717016727International Union of CrystallographyPython-based applications streamline stock and sample management in a medium-throughput crystallization laboratory and yield information as to what chemicals are used in crystallization trial optimization.ENsample managementstock managementcrystallization stocksManaging chemical stocks and samples in any laboratory is an arduous task; in a crystallization laboratory this is particularly burdensome, given the need for many stocks to facilitate optimization of crystal hits obtained from screening experiments. Although inventory management is widespread in retail and other arenas, most small academic laboratories do not adopt formal stock management systems. Without an overarching system for handling stocks and samples, problems such as stock duplication, inappropriate stock storage and insufficient labelling are rife. Two applications have been developed in the Collaborative Crystallization Centre, the first of which manages the hundreds of stocks used for crystallization, and a second which manages protein (and other) samples stored in the 193 K freezer. Both applications are built around a simple database, with a Python front end that allows samples or stocks to be scanned in or out. Information from a decade of crystallization stock usage allows a good estimation of what chemicals are used (and in what quantities) in a crystallization laboratory.text/htmlOrganizing a crystallization laboratorytext1512018-02-01Copyright (c) 2018 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs
http://scripts.iucr.org/cgi-bin/paper?po5112
It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB, `densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.Copyright (c) 2018 International Union of Crystallographyurn:issn:1600-5767Chodkiewicz, M.L.Migacz, S.Rudnicki, W.Makal, A.Kalinowski, J.A.Moriarty, N.W.Grosse-Kunstleve, R.W.Afonine, P.V.Adams, P.D.Dominiak, P.M.2018-02-01doi:10.1107/S1600576717015825International Union of CrystallographyA C++ library for calculation of structure factors from the Hansen–Coppens multipolar model of crystal electron density, featuring parallel implementation for multi-core processors and graphics processing units, is presented.ENstructure factorsrefinementGPUmultipole modelIt has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB, `densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.text/htmlDiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUstext1512018-02-01Copyright (c) 2018 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00CAPOW: a standalone program for the calculation of optimal weighting parameters for least-squares crystallographic refinements
http://scripts.iucr.org/cgi-bin/paper?fs5153
The rigorous analysis of crystallographic models, refined through the use of least-squares minimization, is founded on the expectation that the data provided have a normal distribution of residuals. Processed single-crystal diffraction data rarely exhibit this feature without a weighting scheme being applied. These schemes are designed to reflect the precision and accuracy of the measurement of observed reflection intensities. While many programs have the ability to calculate optimal parameters for applied weighting schemes, there are still programs that do not contain this functionality, particularly when moving beyond the spherical atom model. For this purpose, CAPOW (calculation and plotting of optimal weights), a new program for the calculation of optimal weighting parameters for a SHELXL weighting scheme, is presented and an example of its application in a multipole refinement is given.Copyright (c) 2018 Natalie T. Johnson et al.urn:issn:1600-5767Johnson, N.T.Ott, H.Probert, M.R.2018-02-01doi:10.1107/S1600576717016600International Union of CrystallographyA new standalone program to calculate optimized values for weighting parameters, CAPOW, is presented along with enhanced visualization tools for analysing statistical distributions of data.ENcharge densitymultipolar refinementweightingThe rigorous analysis of crystallographic models, refined through the use of least-squares minimization, is founded on the expectation that the data provided have a normal distribution of residuals. Processed single-crystal diffraction data rarely exhibit this feature without a weighting scheme being applied. These schemes are designed to reflect the precision and accuracy of the measurement of observed reflection intensities. While many programs have the ability to calculate optimal parameters for applied weighting schemes, there are still programs that do not contain this functionality, particularly when moving beyond the spherical atom model. For this purpose, CAPOW (calculation and plotting of optimal weights), a new program for the calculation of optimal weighting parameters for a SHELXL weighting scheme, is presented and an example of its application in a multipole refinement is given.text/htmlCAPOW: a standalone program for the calculation of optimal weighting parameters for least-squares crystallographic refinementstext1512018-02-01Copyright (c) 2018 Natalie T. Johnson et al.Journal of Applied Crystallographycomputer programs00