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: The first well defined cationic terminal hydrido rare earth complexes were isolated from THF, which on recrystallization from chlorobenzene gave reversibly the novel dicationic binuclear dihydride complexes.
32 citations
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TL;DR: In this paper, a general theory as well as a measurement strategy is introduced, allowing extraction of quantitative small-angle scattering information such as structure sizes and scattering cross sections, and the validity of the description is demonstrated by a specific example from literature.
Abstract: Dark-field contrast imaging with grating interferometers has proven to hold huge potential for numerous applications with X-rays and with neutrons conveying biology and medicine as well as engineering and magnetism, respectively. However, a concept to extract quantitative information is still missing. Here a general theory as well as a measurement strategy is introduced, allowing extraction of quantitative small-angle scattering information such as structure sizes and scattering cross sections. The validity of the description is demonstrated by a specific example from literature.
32 citations
TL;DR: A new redox-active ligand, tris(4-(pyridin-4-yl)phenyl)amine (Npy3), has been synthesised, and incorporated into the coordination framework [Cu(Npy 3)Cl2]·DMF, enabling chemical oxidation of the framework.
Abstract: A new redox-active ligand, tris(4-(pyridin-4-yl)phenyl)amine (Npy3), has been synthesised, and incorporated into the coordination framework [Cu(Npy3)Cl2]·DMF. The monoradical cation of the ligand is readily accessible, thus enabling chemical oxidation of the framework. The novel Npy3 ligand has significant potential as a structural motif for the development of multifunctional frameworks.
32 citations
TL;DR: The TEXTAL system represents a new approach to protein structure determination and has the potential to greatly reduce the time required to interpret electron-density maps in order to build accurate protein models.
Abstract: TEXTAL is an automated system for building protein structures from electron-density maps. It uses pattern recognition to select regions in a database of previously determined structures that are similar to regions in a map of unknown structure. Rotation-invariant numerical values, called features, of the electron density are extracted from spherical regions in an unknown map and compared with features extracted around regions in maps generated from a database of known structures. Those regions in the database that match best provide the local coordinates of atoms and these are accumulated to form a model of the unknown structure. Similarity between the regions in the database and an uninterpreted region is determined firstly by evaluating the numerical difference in feature values and secondly by calculating the electron-density correlation coefficient for those regions with similar feature values. TEXTAL has been successful at building protein structures for a wide range of test electron-density maps and can automatically model entire protein structures in a few hours on a workstation. Models built by TEXTAL from test electron-density maps of known protein structures were accurate to within 0.6–0.7 A root-mean-square deviation, assuming prior knowledge of Cα positions. The system represents a new approach to protein structure determination and has the potential to greatly reduce the time required to interpret electron-density maps in order to build accurate protein models.
32 citations
TL;DR: Structural changes that occur during the [2 + 2] photodimerization of the metastable alpha'-polymorph of ortho-ethoxy-trans-cinnamic acid at 293 K are presented here.
Abstract: Structural changes that occur during the [2 + 2] photodimerization of the metastable α′-polymorph of ortho-ethoxy-trans-cinnamic acid at 293 K are presented here. Crystals of the α′-polymorph were first stabilized by exposing the α-polymorph to UV light for a short period of time at 343 K. The photodimerization reaction was then carried out at 293 K and observed in situ by single-crystal X-ray diffraction. The α′-polymorph contains three molecules in the asymmetric unit, labelled A, B and C, which are arranged to form two potential reaction sites. The intermolecular distance between the C=C bonds of molecules A and B (making up the AB site) is 3.6 A, and these were observed to undergo photodimerization at 293 K. The corresponding distance between centrosymmetrically related C=C bonds in the CC site (made up of C molecules) is 4.6 A, and these remain unreacted even after 60 h irradiation at 293 K. The crystal of the final product, which corresponds to a 66.7% conversion (only two out of three molecules in the asymmetric unit take part in the photodimerization reaction at 293 K), contains an ordered arrangement of the photodimer and unreacted monomer. The crystal retains many structural features of the original monomer crystal, including carboxylic acid hydrogen bonds and C—H⋯O interactions. Single-crystal X-ray diffraction was used to monitor changes in the unit-cell parameters, reacting molecules and molecular conformations as the reaction progressed. The conformation of the photodimer obtained from the solid-state reaction differs from that of the photodimer obtained by recrystallization from solution.
32 citations