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: First real-time studies of ultra-fast processes by means of a single-bunch imaging technique at the European Synchrotron Radiation Facility are reported.
Abstract: First real-time studies of ultra-fast processes by single-bunch imaging at the European Synchrotron Radiation Facility are reported. By operating the storage ring of the ESRF in single-bunch mode with its correspondingly increased electron bunch charge density per singlet, the polychromatic photon flux density at insertion-device beamlines is sufficient to capture hard X-ray images exploiting the light from a single bunch (the corresponding bunch length is 140 ps FWHM). Hard X-ray imaging with absorption contrast as well as phase contrast in combination with large propagation distances is demonstrated using spatial samplings of 11 µm and 35 µm pixel size. The images acquired allow one to track crack propagation in a bursting piece of glass, breaking of an electrical fuse as well as cell wall rupture in an aqueous foam. Future developments and their potential in the frame of the proposed Phase II of the ESRF Upgrade Program are discussed.
49 citations
TL;DR: In this paper, the authors investigated the evolution of the stress-induced, reversible transformation between austenite and martensite to determine the cause of the changes in the macroscopic stress-strain response with cycling.
Abstract: Superelastic NiTi was subjected to simultaneous neutron diffraction and uniaxial compressive cycling between 10 and 980 MPa. The objective was an in-situ investigation of the evolution of the stress-induced, reversible transformation between austenite and martensite, to determine the cause of the changes in the macroscopic stress-strain response with cycling. Rietveld refinement was used to analyze the neutron spectra and quantify the phase fraction, texture, and elastic strain. The average phase strain in the mechanically loaded austenite (at a given stress) remained unaltered during the 100 load-unload cycles. However, differences in both the volume fraction and texture of austenite and martensite were noted as cycling progressed, suggesting that these factors are responsible for the changes in the macroscopic stress-strain response of NiTi with mechanical cycling.
49 citations
TL;DR: In this article, a modification of the gel acupuncture method is presented to grow isolated crystals inside X-ray capillaries without any post-crystallization manipulation, and two additional elements are proposed for inclusion in the cryosystems currently in use: a laser pointer to illuminate the crystal to be flash-cooled and a trap to divert the N2 flow and switch from room temperature to 100
Abstract: This paper presents a modification of the gel acupuncture method to grow isolated crystals inside X-ray capillaries. Protein crystals are grown from 2–12 µl of gelled agarose–protein solution, cryoprotected and immobilized by the gel matrix. The same X-ray capillary that acts as a crystallization reactor is used to transport the crystals to the X-ray source and to collect data at both room temperature and 100 K, without any post-crystallization manipulation. To enhance the flash-cooling stage, two additional elements are proposed for inclusion in the cryosystems currently in use: a laser pointer to illuminate the crystal to be flash-cooled and a trap to divert the N2 flow and switch from room temperature to 100 K without misalignment of the crystal. With the proposed implementation, data can be collected at different temperatures from the same crystal in exactly the same orientation. This permits the study, at lattice level, of changes in unit-cell parameters, mosaic spread and crystal quality induced by cryogenic temperatures and annealing techniques.
49 citations
TL;DR: In this paper, the authors present a tool for a group-theoretical analysis of a structural phase transition, including a detailed group±subgroup description of the chain G > H and a calculation of the primary and secondary modes for the symmetry break G! H.
Abstract: Group-theoretical methods are widely used in the investigation of phase transitions in crystals. On the one hand, important structural aspects concerning the relation between the lowand the highsymmetry structures follows from the the group±subgroup relations of the space groups G > H describing the symmetry of the two phases. For example, the number of low-symmetry domain states equals the index of H in the parent group G, while their symmetry groups are conjugate subgroups Hj (isomorphic to H) of G. The splitting schemes of the occupied atomic orbits for the symmetry break G > H (known also as splitting of Wyckoff positions) determine the structural relation between the two phases. Further, an essential feature of a continuous or quasicontinuous displacive phase transition is the appearance of a symmetry-breaking distortion in the low-symmetry phase (with respect to the highsymmetry one) which is mainly caused by the freezing of some mode, the so-called primary mode. In addition, secondary modes are also triggered by the phase transition and can also have non-zero spontaneous amplitudes in the distorted structure. The so-called symmetry-mode analysis allows the `separation' of the frozen primary mode from the contributions of modes of different symmetry present as a secondary effect, but for its application it is necessary ®rst to calculate the symmetry modes of the parent phase, compatible with the low-symmetry phase, and then using their orthonormality properties to decompose the global distortion as a sum of the contributions of each of them. Such a symmetry analysis of phase-transition phenomena is rather complex as it requires full use of group-theoretical methods, including detailed knowledge of the group±subgroup relations of space groups and their irreducible representations (`irreps'). The goal of the developed software package SYMMODES is to provide the necessary tools for a group-theoretical analysis of a structural phase transition, including (i) a detailed group±subgroup description of the chain G > H and (ii) a calculation of the primary and secondary modes for the symmetry break G ! H.
49 citations
TL;DR: The structure of Pfu elucidates the electron density of the interface between the exonuclease and thumb domains, which has not been previously observed in the KOD1 structure, and shows that both the Y-GG/A and beta-hairpin motifs of P Fu are found to differ with that of K OD1, and may explain differences in processivity.
49 citations