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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01 Feb 1999
TL;DR: In this article, the relationship between parameters obtained by the Warren-Averbach approximation and integral-breadth methods becomes possible and the consequences of an assumed Voigt-function profile shape for both sizebroadened and strain-broadened profiles (double-Voigt method) are studied.
Abstract: Diffraction-line broadening routes are briefly reviewed. Both laboratory and synchrotron xray measurements of W and MgO showed that a Voigt function satisfactorily fits the physicall y broadened line profiles. The consequences of an assumed Voigt-function profile shape for both sizebroadened and strain-broadened profiles (“double-Voigt” method) are studied. It is shown that th e relationship between parameters obtained by the Warren-Averbach approximation and integralbreadth methods becomes possible. Line-broadening analysis of W and MgO is performed by using the Warren-Averbach and "double-Voigt" approaches and results are compared.
162 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...After Langford (1978) introduced a Voigt function in the field of x-ray powder diffraction, it was quickly adopted in the Rietveld analysis (Ahtee et al. 1984), along with its approximations (Young and Wiles 1982)....
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TL;DR: A comprehensive description of the methods used within the DIALS framework for diffraction-geometry refinement using predicted reflection centroids is given.
Abstract: Rapid data collection and modern computing resources provide the opportunity to revisit the task of optimizing the model of diffraction geometry prior to integration. A comprehensive description is given of new software that builds upon established methods by performing a single global refinement procedure, utilizing a smoothly varying model of the crystal lattice where appropriate. This global refinement technique extends to multiple data sets, providing useful constraints to handle the problem of correlated parameters, particularly for small wedges of data. Examples of advanced uses of the software are given and the design is explained in detail, with particular emphasis on the flexibility and extensibility it entails.
161 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...This is a useful distinction, because for rotation-scan data these parameters do not alter the central impacts determining the recorded reflection position, only the general impacts that determine the reflection extent (Duisenberg et al., 2003)....
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TL;DR: A nitrogen-rich trefoil hexacarboxylate (trigonal tri-isophthalate) ligand is designed, which serves to act as the trigonal molecular building block while concurrently coding the formation of the targeted truncated cuboctahedral supermolecular building block (in situ), and enhancing the CO(2) uptake in the resultant rht-MOF.
161 citations
TL;DR: A formula for absolute scattering power is derived to include spot fading arising from radiation damage and the crystal volume needed to collect diffraction data to a given resolution is calculated.
Abstract: In this work, classic intensity formulae were united with an empirical spot-fading model in order to calculate the diameter of a spherical crystal that will scatter the required number of photons per spot at a desired resolution over the radiation-damage-limited lifetime. The influences of molecular weight, solvent content, Wilson B factor, X-ray wavelength and attenuation on scattering power and dose were all included. Taking the net photon count in a spot as the only source of noise, a complete data set with a signal-to-noise ratio of 2 at 2 A resolution was predicted to be attainable from a perfect lysozyme crystal sphere 1.2 µm in diameter and two different models of photoelectron escape reduced this to 0.5 or 0.34 µm. These represent 15-fold to 700-fold less scattering power than the smallest experimentally determined crystal size to date, but the gap was shown to be consistent with the background scattering level of the relevant experiment. These results suggest that reduction of background photons and diffraction spot size on the detector are the principal paths to improving crystallographic data quality beyond current limits.
160 citations
Cites result from "J. Appl. Cryst.の発刊に際して"
...This graph is similar to the ‘IE’ quantity obtained by Arndt (1984), except that here the y axis is on an absolute scale....
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TL;DR: The design, performance and first results of the new macromolecular crystallography beamline BL13-XALOC at the ALBA Synchrotron are described, including new developments in optics and control.
Abstract: BL13-XALOC is currently the only macromolecular crystallography beamline at the 3 GeV ALBA synchrotron near Barcelona, Spain. The optics design is based on an in-vacuum undulator, a Si(111) channel-cut crystal monochromator and a pair of KB mirrors. It allows three main operation modes: a focused configuration, where both mirrors can focus the beam at the sample position to 52 µm × 5.5 µm FWHM (H × V); a defocused configuration that can match the size of the beam to the dimensions of the crystals or to focus the beam at the detector; and an unfocused configuration, where one or both mirrors are removed from the photon beam path. To achieve a uniform defocused beam, the slope errors of the mirrors were reduced down to 55 nrad RMS by employing a novel method that has been developed at the ALBA high-accuracy metrology laboratory. Thorough commissioning with X-ray beam and user operation has demonstrated an excellent energy and spatial stability of the beamline. The end-station includes a high-accuracy single-axis diffractometer, a removable mini-kappa stage, an automated sample-mounting robot and a photon-counting detector that allows shutterless operation. The positioning tables of the diffractometer and the detector are based on a novel and highly stable design. This equipment, together with the operation flexibility of the beamline, allows a large variety of types of crystals to be tackled, from medium-sized crystals with large unit-cell parameters to microcrystals. Several examples of data collections measured during beamline commissioning are described. The beamline started user operation on 18 July 2012.
159 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Typically a fluorescence scan takes 100 s and the fluorescence data are processed automatically after the scan with CHOOCH (Evans & Pettifer, 2001)....
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References
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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.
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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.
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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.
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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.
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