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.
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TL;DR: In this article, the authors review techniques that can be used to study the mesoscopic crystallographic structure of grain boundary networks and summarize current findings, showing that grain surfaces within dense polycrystals favor the same low energy planes that are found on equilibrium crystal shapes and growth forms of crystals in contact with another phase.
Abstract: Recent advances both in experimental instrumentation and computing power have made it possible to interrogate the distribution of internal interfaces in polycrystals and the three dimensional structure of the grain boundary network with an unprecedented level of detail. The purpose of this paper is to review techniques that can be used to study the mesoscopic crystallographic structure of grain boundary networks and to summarize current findings. Recent studies have shown that grain surfaces within dense polycrystals favor the same low energy planes that are found on equilibrium crystal shapes and growth forms of crystals in contact with another phase. In the materials for which comprehensive data exists, the distribution of grain boundaries is inversely correlated to the sum of the energies of the surfaces of the grains on either side of the boundary.
236 citations
TL;DR: The RCSB Protein Data Bank has a number of options for deposition of structural data and has developed software tools to facilitate the process and a new software application, pdb_extract, has been designed to promote automatic data deposition of structures solved by X-ray diffraction.
Abstract: The RCSB Protein Data Bank (PDB) has a number of options for deposition of structural data and has developed software tools to facilitate the process. In addition to ADIT and the PDB Validation Suite, a new software application, pdb_extract, has been designed to promote automatic data deposition of structures solved by X-ray diffraction. The pdb_extract software can extract information about data reduction, phasing, molecular replacement, density modification and refinement from the output files produced by many X-ray crystallographic applications. The options, procedures and tools for accurate and automated PDB data deposition are described here.
234 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Presently, validation reports from SFCHECK (Vaguine et al., 1999), PROCHECK (Laskowski et al., 1993) and NUCHECK (Feng et al., 1998) are also produced....
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TL;DR: A report on the characterization, calibration and performances of the MYTHEN photon-counting silicon microstrip detector at the powder diffraction station at the Swiss Light Source is given.
Abstract: The MYTHEN single-photon-counting silicon microstrip detector has been developed at the Swiss Light Source for time-resolved powder diffraction experiments. An upgraded version of the detector has been installed at the SLS powder diffraction station allowing the acquisition of diffraction patterns over 120° in 2θ in fractions of seconds. Thanks to the outstanding performance of the detector and to the calibration procedures developed, the quality of the data obtained is now comparable with that of traditional high-resolution point detectors in terms of FWHM resolution and peak profile shape, with the additional advantage of fast and simultaneous acquisition of the full diffraction pattern. MYTHEN is therefore optimal for time-resolved or dose-critical measurements. The characteristics of the MYTHEN detector together with the calibration procedures implemented for the optimization of the data are described in detail. The refinements of two known standard powders are discussed together with a remarkable application of MYTHEN to organic compounds in relation to the problem of radiation damage.
233 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...17, 653–668 alignment is essential, at least when the intrinsic microstructural broadening is not large. axial is due to the detector and sample axial dimension, known as the Finger–Cox–Jephcoat (FCJ) lineshape (Finger et al., 1994), whose contribution axial is proportional to cot( )....
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TL;DR: This paper accompanies a lecture given at the 2003 CCP4 Study Weekend on experimental phasing with an overview of the fundamentals of Patterson methods and direct methods and a new hybrid substructure search is outlined.
Abstract: This paper accompanies a lecture given at the 2003 CCP4 Study Weekend on experimental phasing. The first part is an overview of the fundamentals of Patterson methods and direct methods with the audience of the CCP4 Study Weekend in mind. In the second part, a new hybrid substructure search is outlined.
232 citations
TL;DR: The accuracy of 215 experimental organic crystal structures from powder diffraction data is validated against a dispersion-corrected density functional theory method.
Abstract: In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 A for SX structures to 0.35 A for XRPD structures; the grey area must be extended from 0.30 to 0.40 A. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.
232 citations
References
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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
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
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
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
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