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: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
Abstract: An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
81,116 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...These days such padding is less desirable and there are excellent programs such as enCIFer (Allen et al., 2004) for working with CIF files, so CIFTAB is now effectively redundant....
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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
Cites methods from "J. Appl. Cryst.の発刊に際して"
...This dictionary contains among oth i ems descriptions of the solution components, the experime conditions, enumerated lists of the instruments used, as we information about structure refinement....
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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.
28,425 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Multithreading is achieved using OpenMP along the lines suggested by Diederichs (2000), and the program is particularly suitable for multiple-core processors....
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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
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...…e-mail: emsley@ysbl.york.ac.uk # 2004 International Union of Crystallography Printed in Denmark ± all rights reserved 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…...
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...The introduction of FRODO (Jones, 1978) and then O (Jones et al., 1991) to the ®eld of protein crystallography was in each case revolutionary, each in their time breaking new ground in demonstrating what was possible with the current hardware....
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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.
18,531 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...After ensuring that the diffraction data are sound and understood, the next critical necessity for solving a structure is the determination of phases using one of several strategies (Adams, Afonine et al., 2009)....
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...Tools such as efficient rigid-body refinement (multiplezones algorithm; Afonine et al., 2009), simulated-annealing refinement (Brünger et al., 1987) in Cartesian or torsion-angle space (Grosse-Kunstleve et al., 2009), automatic NCS detection and its use as restraints in refinement are important at…...
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References
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TL;DR: Symmetry and physical aspects of 'forbidden' reflections excited by a local polarization anisotropy of the X-ray susceptibility are surveyed and the local ;chirality' of atoms in centrosymmetric crystals is accessible.
Abstract: Symmetry and physical aspects of `forbidden' reflections excited by a local polarization anisotropy of the X-ray susceptibility are surveyed. Such reflections are observed near absorption edges where the anisotropy is caused by distortions of the atomic electronic states owing to interaction with neighbouring atoms. As a consequence, they allow for extracting nontrivial information about the resonant atom's local environment and their physical conditions. The unusual polarization properties of the considered reflections are helpful to distinguish them from other types of `forbidden' reflections. When such reflections are excited, it is, for example, possible to determine not only the intrinsic anisotropy of an atomic form factor but also additional anisotropy induced by thermal motion, point defects and/or incommensurate modulations. Even the local `chirality' of atoms in centrosymmetric crystals is accessible. Unsolved key problems and possible future developments are addressed.
106 citations
TL;DR: X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution and a detailed description and comparison of the structures is made with reference to the previously reported structure refined at 2.0 A resolution.
Abstract: X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 Aresolution, respectively, using synchrotron radiation. Data from one crystal were sufficient for the low-temperature study, whereas three crystals were required at room tempera- ture. Refinement was carried out using the programs PROLSQ, ARP and SHELXL to give final conventional R factors of 8.98 and 10.48% for data with F > 4OFU for the low- and room-temperature structures, respec- tively. The estimated r.m.s. coordinate error is 0.032 A ˚ for protein atoms, 0.050 Afor all atoms in the low- temperature study, and 0.038 Afor protein atoms and 0.049 Afor all atoms in the room-temperature case, as estimated from inversion of the blocked least-squares matrix. The low-temperature study revealed that the side chains of 24 amino acids had multiple conforma- tions. A total of 250 waters, six nitrate ions and three acetate ions, two of which were modelled with alternate orientations were located in the electron-density maps. Three sections of the main chain were modelled in alternate conformations. The room-temperature study produced a model with multiple conformations for eight side chains and a total of 139 water molecules, six nitrate but no acetate ions. The occupancies of the water molecules were refined in both structures and this step was shown to be meaningful when assessed by use of the free R factor. A detailed description and comparison of the structures is made with reference to the previously reported structure refined at 2.0 Aresolution.
106 citations
TL;DR: The representation of crystallographic model characteristics in the form of a polygon allows the quick comparison of a model with a set of previously solved structures.
Abstract: A crystallographic macromolecular model is typically characterized by a list of quality criteria, such as R factors, deviations from ideal stereochemistry and average B factors, which are usually provided as tables in publications or in structural databases. In order to facilitate a quick model-quality evaluation, a graphical representation is proposed. Each key parameter such as R factor or bond-length deviation from `ideal values' is shown graphically as a point on a `ruler'. These rulers are plotted as a set of lines with the same origin, forming a hub and spokes. Different parts of the rulers are coloured differently to reflect the frequency (red for a low frequency, blue for a high frequency) with which the corresponding values are observed in a reference set of structures determined previously. The points for a given model marked on these lines are connected to form a polygon. A polygon that is strongly compressed or dilated along some axes reveals unusually low or high values of the corresponding characteristics. Polygon vertices in `red zones' indicate parameters which lie outside typical values.
106 citations
Book•
15 Nov 2017TL;DR: Results for the specimen containing two related high-Tc phases indicate a possible mechanism for the phase transformation by the growth of faulted regions of the major phase and a method to analyze powder-diffraction line broadening.
Abstract: A method to analyze powder-diffraction line broadening is proposed and applied to some novel high-Tc superconductors. Assuming that both size-broadened and strain-broadened profiles of the pure-specimen profile are described with a Voigt function, it is shown that the analysis of Fourier coefficients leads to the Warren-Averbach method of separation of size and strain contributions. The analysis of size coefficients shows that the "hook" effect occurs when the Cauchy content of the size-broadened profile is underestimated. The ratio of volume-weighted and surface-weighted domain sizes can change from ~1.31 for the minimum allowed Cauchy content to 2 when the size-broadened profile is given solely by a Cauchy function. If the distortion co-efficient is approximated by a harmonic term, mean-square strains decrease linearly with the increase of the averaging distance. The local strain is finite only in the case of pure-Gauss strain broadening because strains are then independent of averaging distance. Errors of root-mean-square strains as well as domain sizes were evaluated. The method was applied to two cubic structures with average volume-weighted domain sizes up to 3600 A, as well as to tetragonal and orthorhombic (La-Sr)2CuO4, which exhibit weak line broadenings and highly overlapping reflections. Comparison with the integral-breadth methods is given. Reliability of the method is discussed in the case of a cluster of the overlapping peaks. The analysis of La2CuO4 and La1.85M0.15CuO4(M = Ca, Ba, Sr) high-Tc superconductors showed that microstrains and incoherently diffracting domain sizes are highly anisotropic. In the superconductors, stacking-fault probability increases with increasing Tc; microstrain decreases. In La2CuO4, different broadening of (h00) and (0k0) reflections is not caused by stacking faults; it might arise from lower crystallographic symmetiy. The analysis of Bi-Cu-O superconductors showed much higher strains in the [001] direction than in the basal a-b plane. This may be caused by stacking disorder along the c-axis, because of the two-dimensional weakly bonded BiO double layers. Results for the specimen containing two related high-Tc phases indicate a possible mechanism for the phase transformation by the growth of faulted regions of the major phase.
105 citations
TL;DR: In this paper, a synchrotron X-ray transmission technique was applied to study the internal load transfer and micromechanical damage in molybdenum particle-reinforced copper matrix composites during plastic deformation.
Abstract: A synchrotron X-ray transmission technique was applied to study the internal load transfer and micromechanical damage in molybdenum particle-reinforced copper matrix composites during plastic deformation. Mechanically loaded, 1.5-mm-thick specimens were irradiated with a monochromatic beam of 65 keV X-rays. Low-index diffraction rings of both phases were recorded with a high-resolution two-dimensional detector. By means of newly developed data processing routines, we could quantify as a function of applied stress both the ring distortion (from which the volume-averaged elastic strains in the two phases were calculated), and the ring graininess (which is related to the Bragg peak broadening). Based on this information, the deformation and damage processes in these alloys were studied in detail. As compared to conventional neutron diffraction methods, the photon transmission technique yielded similar precision but at much reduced measurement times. The main sources of experimental errors were identified and strategies to minimize these errors were developed.
105 citations