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Journal ArticleDOI

J. Appl. Cryst.の発刊に際して

10 Mar 1970-Vol. 12, Iss: 1, pp 1-1
About: The article was published on 1970-03-10 and is currently open access. It has received 8159 citations till now.
Citations
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Journal ArticleDOI
TL;DR: In this article, the texture analysis of hot-rolled polycrystalline zirconium has been studied below and above the hcp-bcc transition temperature with HIPPO at Los Alamos Neutron Science Center, making use of the multidetector capabilities and a vacuum furnace.

91 citations


Cites methods from "J. Appl. Cryst.の発刊に際して"

  • ...In this report we will first describe the experiment and data processing, then present the results and finally apply modelling to quantify the variant selection and propose a plausible explanation....

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Journal ArticleDOI
TL;DR: In this paper, the authors demonstrate anti-inflammatory effects of strontium for human monocytes cultured in contact with calcium phosphates using synchrotron powder diffraction data.
Abstract: Sol–gel chemistry has been successfully used to prepare un-doped and Sr-doped calcium phosphate ceramics exhibiting a porous structure. The samples composition is very close to the nominal one. All samples present phase mixtures of mainly hydroxyapatite (HAp) and tricalcium phosphate (β-TCP). Doping with Sr2+ ions has a clear effect on the proportions of the different phases, increasing the amount of β-TCP. An amorphous phase is also observed incorporating some 40% of the total amount of strontium. Strontium ions also substitute for calcium both in HAp and β-TCP in specific sites that have been determined from Rietveld refinement on synchrotron powder diffraction data. The soluble amorphous and TCP phases are responsible for a beneficial partial release of strontium ions in solution during interactions between the material and biological fluids. Preliminary in vitro study demonstrates anti-inflammatory effects of strontium for human monocytes cultured in contact with calcium phosphates.

91 citations

Journal ArticleDOI
TL;DR: The development of a model for determining the photon flux incident on pin diodes, and experiments to test this model, are described for incident energies between 4 and 18 keV used in macromolecular crystallography.
Abstract: Accurate measurement of photon flux from an X-ray source, a parameter required to calculate the dose absorbed by the sample, is not yet routinely available at macromolecular crystallography beamlines. The development of a model for determining the photon flux incident on pin diodes is described here, and has been tested on the macromolecular crystallography beamlines at both the Swiss Light Source, Villigen, Switzerland, and the Advanced Light Source, Berkeley, USA, at energies between 4 and 18 keV. These experiments have shown that a simple model based on energy deposition in silicon is sufficient for determining the flux incident on high-quality silicon pin diodes. The derivation and validation of this model is presented, and a web-based tool for the use of the macromolecular crystallography and wider synchrotron community is introduced.

90 citations


Cites background or methods from "J. Appl. Cryst.の発刊に際して"

  • ...The silicon photodiode is such a device (Jach & Cowan, 1983; Krumrey et al., 2006; Alkire & Rotella, 1997)....

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  • ...DE-AC03-76SF00098 at Lawrence Berkeley National Laboratory....

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  • ...A comparison of various diodes of different types and thicknesses carried out both at the Advanced Light Source (ALS, Berkeley, USA) and the Swiss Light Source (SLS, Villigen, Switzerland) is presented here, as well as a model by which flux can most easily be quantified to enable accurate MX dose…...

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  • ...The development of a model for determining the photon flux incident on pin diodes is described here, and has been tested on the macromolecular crystallography beamlines at both the Swiss Light Source, Villigen, Switzerland, and the Advanced Light Source, Berkeley, USA, at energies between 4 and 18 keV....

    [...]

  • ...16, 143–151 doi:10.1107/S0909049508040429 143 Journal of Synchrotron Radiation ISSN 0909-0495 Received 2 September 2008 Accepted 26 November 2008 Determination of X-ray flux using silicon pin diodes Robin L. Owen,a‡2James M. Holton,b,c Clemens Schulze-Briesea and Elspeth F. Garmand* aSwiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland, bDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2330, USA, cAdvanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, and dLaboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK....

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Journal ArticleDOI
TL;DR: The mapping of structure sets to fingerprint space could become a new paradigm for studying crystal-structure ensembles and global chemical features of the energy landscape.
Abstract: The initial aim of the crystal fingerprint project was to solve a very specific problem: to classify and remove duplicate crystal structures from the results generated by the evolutionary crystal-structure predictor USPEX. These duplications decrease the genetic diversity of the population used by the evolutionary algorithm, potentially leading to stagnation and, after a certain time, reducing the likelihood of predicting essentially new structures. After solving the initial problem, the approach led to unexpected discoveries: unforeseen correlations, useful derived quantities and insight into the structure of the overall set of results. All of these were facilitated by the project's underlying idea: to transform the structure sets from the physical configuration space to an abstract, high-dimensional space called the fingerprint space. Here every structure is represented as a point whose coordinates (fingerprint) are computed from the crystal structure. Then the space's distance measure, interpreted as structure `closeness', enables grouping of structures into similarity classes. This model provides much flexibility and facilitates access to knowledge and algorithms from fields outside crystallography, e.g. pattern recognition and data mining. The current usage of the fingerprint-space model is revealing interesting properties that relate to chemical and crystallographic attributes of a structure set. For this reason, the mapping of structure sets to fingerprint space could become a new paradigm for studying crystal-structure ensembles and global chemical features of the energy landscape.

90 citations


Cites background from "J. Appl. Cryst.の発刊に際して"

  • ...The work of Hundt et al. (2006) gives a comprehensive survey of existing methods and is focused on calculating some form of distance measure between structures....

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Journal ArticleDOI
TL;DR: Bonnell et al. as discussed by the authors present the authors' viewpoint on the material characterization field, reviewing its recent past, evaluating its present capabilities, and proposing directions for its future development, including suggestions for instrumentation advances, scientific problems in microstructure analysis, and complex structure evolution problems involving material damage.
Abstract: The material characterization toolbox has recently experienced a number of parallel revolutionary advances, foreshadowing a time in the near future when material scientists can quantify material structure evolution across spatial and temporal space simultaneously. This will provide insight to reaction dynamics in four-dimensions, spanning multiple orders of magnitude in both temporal and spatial space. This study presents the authors’ viewpoint on the material characterization field, reviewing its recent past, evaluating its present capabilities, and proposing directions for its future development. Electron microscopy; atom probe tomography; x-ray, neutron and electron tomography; serial sectioning tomography; and diffraction-based analysis methods are reviewed, and opportunities for their future development are highlighted. Advances in surface probe microscopy have been reviewed recently and, therefore, are not included [D.A. Bonnell et al.: Rev. Modern Phys. in Review]. In this study particular attention is paid to studies that have pioneered the synergetic use of multiple techniques to provide complementary views of a single structure or process; several of these studies represent the state-of-the-art in characterization and suggest a trajectory for the continued development of the field. Based on this review, a set of grand challenges for characterization science is identified, including suggestions for instrumentation advances, scientific problems in microstructure analysis, and complex structure evolution problems involving material damage. The future of microstructural characterization is proposed to be one not only where individual techniques are pushed to their limits, but where the community devises strategies of technique synergy to address complex multiscale problems in materials science and engineering.

89 citations

References
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Journal ArticleDOI
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

34,239 citations

Journal ArticleDOI
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

28,425 citations

Journal ArticleDOI
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.

27,505 citations

Journal ArticleDOI
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. How­ever, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallo­graphic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

18,531 citations

Journal ArticleDOI
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

17,755 citations