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Journal Article•DOI•

J. Appl. Cryst.の発刊に際して

良二 上田
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.
Citations
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Journal Article•DOI•
The introduction of structure types into the Inorganic Crystal Structure Database ICSD

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Rudolf Allmann, Roland Hinek
01 Sep 2007-Acta Crystallographica Section A
TL;DR: The approach used and the progress made in the assignment of structure types to the crystal structures contained in the ICSD database are reported.
Abstract: Both the approach used and the progress made in the assignment of structure types to the crystal structures contained in the ICSD database are reported. Extending earlier work, an hierarchical set of criteria for the separation of isopointal structures into isoconfigurational structure types is used. It is shown how these criteria, which include the space group (number), Wyckoff sequence and Pearson symbol, c/a ratio, β ranges, ANX formulae and, in certain cases, the necessary elements and forbidden elements, may be used to uniquely identify the representative structure types of the compounds contained in the ICSD database.

170 citations

Cites methods from "J. Appl. Cryst.の発刊に際して"

  • ...Searching for structure types in the PC version of FindIt and the Web version of the ICSD...

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  • ...This manifold of equivalent Wyckoff sequences could have been reduced by standardizing all structures in the ICSD using a program such as STRUCTURE TIDY (Gelato & Parthé, 1987), but then relationships to similar structures in different space groups may have been lost....

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  • ...3 In addition, a practical difficulty with the program STRUCTURE TIDY, which works well in about 90% of all cases, is that it does not transform the anisotropic displacement parameters automatically during the cell transformations in the standardization procedure....

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  • ...Finally, we would like to mention that STRUCTURE TIDY has been used for the determination of a standardized setting for a few prototypical structures....

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  • ...For the last example, the 145 isopointal structures were at first standardized by STRUCTURE TIDY....

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Journal Article•DOI•
The termination of the α-Al2O3 (0001) surface: a LEED crystallography determination

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J Toofan1, Philip R. Watson1•
Oregon State University1
01 Apr 1998-Surface Science
TL;DR: In this paper, a tensor low-energy electron diffraction (TLEED) determination of 10 diffracted beams at off-normal incidence from the (0001) surface of α-Al2O3 produced by oxygen plasma cleaning/annealing cycles was performed.

169 citations

Cites methods from "J. Appl. Cryst.の発刊に際して"

  • ...For unit cell parameters, we have used the recent synchrotron data of Thompson et al. [11] In most simple binary oxides, the (1×1) structure , where known [12], is close to a simple truncated bulk structure....

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Journal Article•DOI•
FEM: feature-enhanced map

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Pavel V. Afonine1, Nigel W. Moriarty1, Marat Mustyakimov2, Oleg V. Sobolev1, Thomas C. Terwilliger3, Dušan Turk4, Alexandre Urzhumtsev5, Alexandre Urzhumtsev6, Paul D. Adams7, Paul D. Adams1 •
Lawrence Berkeley National Laboratory1, Oak Ridge National Laboratory2, Los Alamos National Laboratory3, Jožef Stefan Institute4, University of Lorraine5, French Institute of Health and Medical Research6, University of California, Berkeley7
01 Mar 2015-Acta Crystallographica Section D-biological Crystallography
TL;DR: The non-iterative feature-enhancing approach improves crystallographic maps’ interpretability by reducing model bias and noise and strengthening the existing signal.
Abstract: A method is presented that modifies a 2mFobs − DFmodel σA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2mFobs − DFmodel σA-weighted map.

169 citations

Cites background or methods from "J. Appl. Cryst.の発刊に際して"

  • ...(iii) Various kinds of OMIT maps (Bhat & Cohen, 1984; Bhat, 1988; Hodel et al., 1992; Gunčar et al., 2000; Vellieux & Dijkstra, 1997; Terwilliger et al., 2008; Pražnikar et al., 2009; Cowtan, 2012)....

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  • ...In contrast to the classical approach for calculating a composite OMIT map (Bhat & Cohen, 1984; Bhat, 1988), we implemented a procedure that is similar to that described by Cowtan (2012)....

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  • ...For each box, a larger box (wide box) is defined by expanding the original box by one grid node in each direction (the ‘neutral’ volume in Bhat, 1988); the corresponding volumes inside the wide box in the model map and bulk-solvent 652 Afonine et al. Feature-enhanced map Acta Cryst....

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Journal Article•DOI•
Crystallographic refinement of ligand complexes

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Gerard J. Kleywegt1•
Uppsala University1
01 Jan 2007-Acta Crystallographica Section D-biological Crystallography
TL;DR: Methods and resources for obtaining chemically plausible starting models and restraint sets for refinement of ligand complexes are described and some of the potential pitfalls are discussed.
Abstract: Model building and refinement of complexes between biomacromolecules and small molecules requires sensible starting coordinates as well as the specification of restraint sets for all but the most common non-macromolecular entities. Here, it is described why this is necessary, how it can be accomplished and what pitfalls need to be avoided in order to produce chemically plausible models of the low-molecular-weight entities. A number of programs, servers, databases and other resources that can be of assistance in the process are also discussed.

169 citations

Journal Article•DOI•
Halogen bonds in some dihalogenated phenols: applications to crystal engineering

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Arijit Mukherjee1, Gautam R. Desiraju1•
Indian Institute of Science1
01 Jan 2014-IUCrJ
TL;DR: The preference of Br to form type II contacts over type I is explored by various techniques and some dihalogenated phenols are correlated with their structures.

167 citations

Cites methods from "J. Appl. Cryst.の発刊に際して"

  • ...Structure solution and refinements were performed using SHELX97 (Sheldrick, 2008) within the WinGX suite (Farrugia, 1999)....

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References
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Journal Article•DOI•
The Protein Data Bank

[...]

Helen M. Berman1, John D. Westbrook, Zukang Feng, Gary L. Gilliland, Talapady N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne •
Rutgers University1
01 Jan 2000-Nucleic Acids Research
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

Journal Article•DOI•
Crystal structure refinement with SHELXL

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George M. Sheldrick1•
University of Göttingen1
01 Jan 2015-Acta Crystallographica Section C-crystal Structure Communications
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

Journal Article•DOI•
Coot: model-building tools for molecular graphics.

[...]

Paul Emsley1, Kevin Cowtan1•
University of York1
01 Dec 2004-Acta Crystallographica Section D-biological Crystallography
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

Journal Article•DOI•
PHENIX: a comprehensive Python-based system for macromolecular structure solution

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Paul D. Adams1, Paul D. Adams2, Pavel V. Afonine1, Gábor Bunkóczi3, Vincent B. Chen4, Ian W. Davis4, Nathaniel Echols1, Jeffrey J. Headd4, Li-Wei Hung5, Gary J. Kapral4, Ralf W. Grosse-Kunstleve1, Airlie J. McCoy3, Nigel W. Moriarty1, Robert D. Oeffner3, Randy J. Read3, David S. Richardson4, Jane S. Richardson4, Thomas C. Terwilliger5, Peter H. Zwart1 •
Lawrence Berkeley National Laboratory1, University of California, Berkeley2, University of Cambridge3, Duke University4, Los Alamos National Laboratory5
01 Feb 2010-Acta Crystallographica Section D-biological Crystallography
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

Journal Article•DOI•
Phaser crystallographic software

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Airlie J. McCoy1, Ralf W. Grosse-Kunstleve2, Paul D. Adams2, Martyn Winn3, Laurent C. Storoni1, Randy J. Read1 •
University of Cambridge1, Lawrence Berkeley National Laboratory2, Daresbury Laboratory3
01 Aug 2007-Journal of Applied Crystallography
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.

17,755 citations