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: In this paper, a method for fast and non-destructive characterization of individual grains inside bulk materials (powders or polycrystals) is presented, where positions, volumes and orientations of hundreds of grains are determined simultaneously.
Abstract: A method is presented for fast and non-destructive characterization of the individual grains inside bulk materials (powders or polycrystals). The positions, volumes and orientations of hundreds of grains are determined simultaneously. An extension of the rotation method is employed: a monochromatic beam of high-energy X-rays, focused in one dimension, impinges on the sample and the directions of the diffracted beams are traced by translation of two-dimensional detectors. Algorithms suitable for on-line analysis are described, including a novel indexing approach, where the crystal symmetry is used directly by scanning in Euler space. The method is verified with a simulation of 100 grains.
191 citations
TL;DR: Beamline ID23-2, the first dedicated and highly automated high-throughput monochromatic macromolecular crystallography microfocus beamline, is described.
Abstract: The first phase of the ESRF beamline ID23 to be constructed was ID23-1, a tunable MAD-capable beamline which opened to users in early 2004. The second phase of the beamline to be constructed is ID23-2, a monochromatic microfocus beamline dedicated to macromolecular crystallography experiments. Beamline ID23-2 makes use of well characterized optical elements: a single-bounce silicon (111) monochromator and two mirrors in Kirkpatrick–Baez geometry to focus the X-ray beam. A major design goal of the ID23-2 beamline is to provide a reliable, easy-to-use and routine microfocus beam. ID23-2 started operation in November 2005, as the first beamline dedicated to microfocus macromolecular crystallography. The beamline has taken the standard automated ESRF macromolecular crystallography environment (both hardware and software), allowing users of ID23-2 to be rapidly familiar with the microfocus environment. This paper describes the beamline design, the special considerations taken into account given the microfocus beam, and summarizes the results of the first years of the beamline operation.
190 citations
TL;DR: In this paper, a method for estimating the distribution of grain-boundary types in polycrystalline materials on the basis of observations from a single planar section is described.
Abstract: A stereological method is described for estimating the distribution of grain-boundary types in polycrystalline materials on the basis of observations from a single planar section. The grain-boundary distribution is expressed in terms of five macroscopically observable parameters that include: three parameters that describe the lattice misorientation across the boundary and two parameters that describe the orientation of the grain-boundary plane normal. The grain-boundary distribution is derived from measurements of grain orientations and the orientations of the lines formed where grain boundaries intersect the plane of observation. Tests of the method on simulated observations illustrate that the distribution of boundaries in a material with cubic symmetry can be reliably determined with about 10° of resolution from the analysis of 5×104 or more line segments. Furthermore, grain-boundary distributions directly observed from serial sections of a SrTiO3 polycrystal are compared to those resulting from the stereological analysis of a single plane. The comparison shows that the stereological method provides a reasonable estimate of the measured distribution. The differences between the directly observed grain-boundary distribution and that derived from the stereological analysis are consistent with the results from the simulation.
189 citations
01 Feb 2017
TL;DR: The program AceDRG generates accurate stereochemical descriptions, and one or more conformations, of a given ligand, and analyses entries and extracts local environment-dependent atom types, bonds and angles from the Crystallography Open Database.
Abstract: The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the `ideal' bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files.
188 citations
Book•
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31 Aug 2003
TL;DR: The Neutron Data Booklet as mentioned in this paper is a pocketbook that covers the wide field of neutron scattering, which was published by the International Lightweight Laboratory (ILL) in the early 1990s.
Abstract: T o make freely available a small pocketbook that covers the wide field of neutron scattering, is clearly an idea which was timely. The first edition of 5000 copies was absorbed by the growing neutron community worldwide within a few months of being published. The obvious need for a second edition has allowed certain corrections to be made to the first edition – inevitable given the speed with which it was written and printed – and to rectify some omissions – notably a new chapter on diffraction methods on continuous sources by Alan Hewat and Garry McIntyre. I want to thank Christian Vettier, ILL's Science Director, who is at the origin of this project and the two editors Gerry Lander from Kalsruhe and José Dianoux from Grenoble who have energetically pursued and implemented the idea, and of course the authors who have once again responded admirably to a tight deadline. W elcome to the Neutron Data Booklet. The success of the X-ray and Nuclear Physics Booklets, and the ever-increasing number of neutron users, has led the ILL in collaboration with Old City Publishing, to compile this "little book of facts." We are first grateful to Christian Vettier of the ILL who persuaded us to undertake this task and helped in many ways in getting people to cooperate. We thank all those who contributed most sincerely; we realise that this is not a research document, and therefore lacking in real excitement. On the other hand, we hope they (and you the reader) will find it above all "useful" and get to feel that having one in your pocket is part of the dress code for a practicing neutron scatterer. Our thanks to the secretarial help at the ILL, who are listed. They gainfully struggled over tables to format and kept their cool. Although this document was produced at the ILL, we recognise the importance of spallation neutrons, and we hope you will find all you need about neutrons in general in the pages. The editors would like to be informed of both errors and omissions so that these may be corrected in future editions and for when the information is loaded onto the web. In particular, suggestions for further tables or chapters will be warmly received, especially if they are accompanied by a "volunteer author"! Finally, thanks to Ian Mellanby and Guy Griffiths of Old City Publishing for following through with …
187 citations