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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: Quality criteria that help produce automated direct Fourier transformed PDFs of quality similar to hand-processed data are presented, and optimization methods are compared.
Abstract: The introduction of neutron spallation-source instruments, such as the General Materials Diffractometer (GEM) at ISIS, allows measurement of pair distribution function (PDF) data at significantly higher rates than previously possible. As a result of the increased rate, a single experiment can produce over a hundred individual runs. Manual processing of all these data using traditional methods becomes inconvenient and inefficient. This article presents quality criteria that help produce automated direct Fourier transformed PDFs of quality similar to hand-processed data, and compares optimization methods.

104 citations


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

  • ...Many authors have described various techniques for ®nding either an absolute scale factor (Kartha, 1953; Krogh-Moe, 1956; Norman, 1957; Kaszkur, 1990; Cumbrera et al., 1995; Leadbetter & Wright, 1972) or a relative scale factor (Hannon et al., 1990; Soper et al., 1989; Louca & Egami, 1999) to…...

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Journal ArticleDOI
01 Nov 2015-IUCrJ
TL;DR: Supramolecular interactions in the solid state are discussed in the context of crystal engineering, specific topics include halogen bonding, ambient and non-ambient conditions, isostructurality and polymorphism, and kinetic assembly of coordination polymers.

104 citations

Journal ArticleDOI
TL;DR: A system for the automatic reduction of single- and multi-position macromolecular crystallography data is presented and its application in nanofiltration and liquid chromatography is proposed.
Abstract: The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.

104 citations


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

  • ...…Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France, bEuropean Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042, Grenoble, France, and cUnit of Virus Host–Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France....

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Journal ArticleDOI
TL;DR: Single crystals of the title compound, trisodium divanadium(III) tris(orthophosphate), were grown from a self-flux in the system Na4P2O7–NaVP2O8 and found that the two independent Na+ cations are located in channels with two different oxygen environments.
Abstract: Single crystals of the title compound, tris­odium divanadium(III) tris­(orthophosphate), were grown from a self-flux in the system Na4P2O7–NaVP2O7. Na3V2(PO4)3 belongs to the family of NASICON-related structures and is built up from isolated [VO6] octa­hedra (3. symmetry) and [PO4] tetra­hedra (.2 symmetry) inter­linked via corners to establish the framework anion [V2(PO4)3]3−. The two independent Na+ cations are partially occupied [site-occupancy factors = 0.805 (18) and 0.731 (7)] and are located in channels with two different oxygen environments, viz sixfold coordination for the first (\overline{3}. symmetry) and eightfold for the second (.2 symmetry) Na+ cation.

104 citations


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

  • ...For preparation of NaVP2O7 which was used as an educt for crystal growth of the title compound, see: Zatovsky et al. (1999)....

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  • ...…2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 1999); software used to prepare material for publication: WinGX (Farrugia, 1999) and enCIFer (Allen et al., 2004)....

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Journal ArticleDOI
TL;DR: The integration of two Python toolboxes used for processing tomographic data, TomoPy and the ASTRA toolbox, is presented.
Abstract: The processing of tomographic synchrotron data requires advanced and efficient software to be able to produce accurate results in reasonable time. In this paper, the integration of two software toolboxes, TomoPy and the ASTRA toolbox, which, together, provide a powerful framework for processing tomographic data, is presented. The integration combines the advantages of both toolboxes, such as the user-friendliness and CPU-efficient methods of TomoPy and the flexibility and optimized GPU-based reconstruction methods of the ASTRA toolbox. It is shown that both toolboxes can be easily installed and used together, requiring only minor changes to existing TomoPy scripts. Furthermore, it is shown that the efficient GPU-based reconstruction methods of the ASTRA toolbox can significantly decrease the time needed to reconstruct large datasets, and that advanced reconstruction methods can improve reconstruction quality compared with TomoPy's standard reconstruction method.

103 citations


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

  • ...…such as those with extremely high spatial or temporal resolutions (Sakdinawat & Attwood, 2010; Mokso et al., 2013) and of dose-sensitive objects (Lovric et al., 2013), require a variety of pre-processing, post-processing and reconstruction algorithms to reduce artifacts in the final…...

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  • ...…bAdvanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4837, USA, ciMinds–Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium, and dMathematical Institute, Leiden University, Niels Bohrweg 1, 2333 CA Leiden, The Netherlands....

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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