International Union Of Crystallography Research Articles

STAR/mmCIF: an ontology for macromolecular structure.

Crystallographers were motivated 10 years ago to develop a simple and consistent data representation for the exchange and archiving of data associated with the crystallographic experiment and the final structure. As this process evolved (and the data grew at near exponential rates) came the recognition that this representation should also facilitate the automated management of the data and, with the aid of additional software for verification and validation, provide improved consistency and accuracy and hence improved scientific inquiry. This realization led to a new Dictionary Definition Language (DDL) and an extensive dictionary based on this DDL for describing macromolecular structure. In broad terms this could be considered an ontology. An important feature in the development of the ontology was the endorsement and ongoing maintenance and support of the International Union of Crystallography (IUCr). While the description of macromolecular structure and the x-ray crystallographic experiment used to derive it represent explicit data, the ontology is extensible and applicable to other less well-characterized data domains. Details of the DDL, the dictionaries that have been developed, and software for reading and using this ontology are presented. Extensive documentation, software tools and the DDL and dictionaries are available from http://ndbserver.rutgers.edu/mmcif and associated mirror sites. Bourne: bourne@sdsc.edu and Westbrook:jwest@rcsp.rutgers.edu

XAFS x conference in Chicago

On August 10-14, 1998, the 10th International Conference on X-ray Absorption Fine Structure (XAFS X) was held on the Illinois Institute of Technology campus in Chicago. This is one of the major synchrotron radiation conferences, held every two years since 1981 when the first international meeting of XAFS experts was held in Daresbury, coincident with the operation of the first of the second-generation dedicated synchrotron radiation sources. The XAFS conferences have evolved over the years with the more recent conferences covering not only the advances in instrumentation, theory and method but also their applications in disciplines ranging from biological to environmental sciences. Approximately 360 scientists from 23 countries attended the conference. The program consisted of 467 abstracts for plenary talks, invited talks, contributed talks, and posters. The co-chairs for the conference were B. Bunker, S. Heald, and T. Morrison and the Program Chair was J. Penner-Hahn. The first IXS award for career contributions to the field was presented to F. Lytle who gave a plenary talk on 'The EXAFS Family Tree: History of the Development of X-ray Absorption Spectroscopy'. In addition, awards were given for the best poster by a young scientist at each session. The winners were M. Duff,more » D. Cabaret and S. Rossano. The International Union of Crystallography (IUCr) also sponsored poster prizes for the best posters in the areas of biology and instrumentation and methods. These winners were A. Templeton and M. Suzuki.« less

Obituary: David Chilton Phillips (Lord Phillips of Ellesmere), 1924–1999

Obituary: David Chilton Phillips (Lord Phillips of Ellesmere), 1924–1999

Data Languages and Dictionaries for Crystallography

Advances in computing over the last 50 years have profoundly influenced the evolution of crystallography's data-rich and calculation-intensive methodologies. The increasing emphasis on data integrity and accessibility over this period has necessitated, and spawned, new and innovative computer applications. The recent use of universal data languages to facilitate the interchange, publication and archiving of data, and the rigorous definition of data in computer-readable dictionaries, has improved the efficiency of these applications and provided new insights into our science. These developments have been aided by the International Union of Crystallography, which, through its Commissions and journals, plays a leading role in coordinating and promoting information dissemination, data standards, databases and ensuring their convenient access. This paper describes the uses of data languages and dictionaries, with particular reference to the development of the Crystallographic Information File (CIF) which is now widely used in the structural sciences.

Compilation of temperature factors of hexagonal close packed elements

The Commission on Neutron Diffraction has initiated a project for compiling accurate temperature factors [International Union of Crystallography (1985). Acta Cryst. B41, 374]. Recommended values of the temperature factors of 14 hexagonal close packed (h.c.p.) elements are presented in this compilation.

Structure of the calcium-binding echidna milk lysozyme at 1.9 Å Resolution. Erratum

Owing to a printer's error, pages 359 and 360 of this article [Guss, Messer, Costello, Hardy & Kumar (1997). Acta Cryst. D53, 355–363Acta Cryst. D53, 355–363] were incorrectly numbered and thus printed in the wrong order. Revised offprints for this paper are available through the Managing Editor, International Union of Crystallography, 5 Abbey Square, Chester CH 1 2HU, England.

Li+/Na+ β-alumina: a combined single-crystal neutron and X-ray diffraction study. Erratum

Lists of atomic coordinates, anisotropic displacement parameters and structure factors have been deposited with the IUCr (Reference: AB0365) for this article [Edström, Gustafsson, Thomas & Farrington, Acta Cryst. B53, 631–638]. Copies may be obtained through The Managing Editor, International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England.

Computer database of magnetic structures determined by neutron diffraction

In this work a proposal for a magnetic database and its presentation by computer program is given. The source files are organized in a way strictly adhering to CIF standard, accepted by International Union of Crystallography. These files contain information about the paramagnetic phase above the magnetic phase transition, and the magnetically ordered phases below the transition. The magnetic structure description includes the transition temperatures, magnitude of the magnetic moments and their directions. Symmetry-based description is also given. Corresponding references are given for all the information. These informations are presented by a program written in C + +, in text and graphic modes, which provides a possibility to search, to show and print all the information and draw crystallographic and magnetic unit cells.

Book Reviews: The gentle pioneer

P.P. Ewald and his Dynamical Theory of X-ray Diffraction . Edited by D.W.J. Cruickshank, H.J. Juretschke & N. Kato. International Union of Crystallography, Oxford University Press, 1992. Pp. x+161, £40.00. ISBN 0-19-855379-X Paul Ewald, who died in 1985 at the age of 97, was one of the greats of modern science. Born in Berlin into a comfortable middle-class academic family, he developed a passion for mathematical physics. When Sommerfeld presented him with a list of possible topics for his Doctoral Thesis he chose one related to crystal optics. This work, presented in 1912, could be applied to the behaviour of X-rays in crystals and it is suggested that it was a conversation between von Laue and Ewald early in 1912 that gave von Laue the idea for his famous experimental demonstration of X-ray diffraction.

Optimized Schedule for Large Crystallography Meetings

International crystallography meetings like the International Union of Crystallography, European Crystallographic Meetings and American Crystallographic Association ones currently offer very comprehensive programs with four parallel sessions or more over a week or so. Proper scheduling of these sessions is nearly as important for the scientific success of these meetings as the selection of topics. In order to tackle this problem objectively, it is proposed here to poll crystallographers about the sessions they most wish to attend, and to accept that schedule which minimizes the sum of residual conflicts calculated from the results of the poll and also respects a number of constraints. A novel semi-automated optimization in four steps, based on the existence of major interest profiles among participants, was applied to the scheduling of the American Crystallographic Association 1995 Annual Meeting: a simple rearrangement of a `conflict matrix' to produce clusters of sessions with large conflicts, followed by application of constraints within clusters in step 2, then a small number of permutations within clusters only, each of them lowering the sum of conflicts while respecting constraints, and finally assignment of sessions to rooms. Without necessarily producing the absolute best solution, solutions very superior to those from intuition and respecting constraints can be built in this way with limited computing power. The experimental data were taken from 102 replies to an e-mail poll of crystallographers at large. Only 20 permutations were performed in step 3. The solution respected all constraints but one, which was relaxed in order to avoid a bad conflict. At the meeting, the room assignments turned out to be mostly verified, with just a few surprises, all having to do with outstanding contributed talks at sessions with no invited speakers. The total attendance at sessions remained high for the whole duration of the meeting. Calculations were programmed in Fortran and performed on a 386 PC clone.

Diffraction data deposition

A formal discussion of the archival journal requirements for data deposition was held at the International Seminar-cum-School on Macromolecular Crystallographic Data at Calcutta, India in November 1995.The current policy of the International Union of Crystallography (IUCr) is that on publication of a crystal structure determination of a macromolecule the atomic parameters used or represented in the publication must be deposited in the Brookhaven Protein Data Bank. The deposition of structure amplitudes is recommended but not obligatory. The policy provides crystallographers with the option to delay the release of atomic parameters for one year and of structure amplitudes for up to four years from the date of publication. Participants strongly supported this policy and felt it should be strictly applied by the journals.Recent developments in X-ray crystallographic experimental and refinement techniques and the huge expansion in computing power and networking, however, necessitate the review of deposition arrangements.It was noted that the new validation procedures are much more effective but require the experimental structure amplitudes as well as the atomic parameters. In addition, the technical arrangements for deposition, analysis and validation of macromolecular crystal structures are now much easier.We consider it vital for macromolecular crystallographers to respond to these developments in their deposition practices. We recommend, therefore, that publication of macromolecular crystal structures should be accompanied by deposition of atomic parameters and also structure amplitudes. Amongst the many reasons identified for this practice, the following two are critical.(1) Rigorous validation of the structure determination results can only be carried out using both atomic parameters and experimental structure amplitudes. It is important that journals ensure referees have sufficient information to prevent incorrect structures being published.(2) Archiving of these data will ensure that they are not lost. There were numerous reports at this meeting of data being lost. This probably reflects a widespread problem in the crystallographic community.

Structural properties of synthetic ionophore GL 2 E 4 diastereomers, 18-membered cyclic lactone tetraepoxides, by X-ray crystal analyses: possible relation between crystal structure and Ca2+-transportation ability. Addendum

Structure factors, anisotropic displacement parameters, H-atom coordinates and complete geometry for the paper by Doi, In Nishino, Ishida, Inoue, Shibuya, Ohashi, Narita & Kitagawa [Acta Cryst. (1995), B51, 1045–1050] have been deposited with the IUCr (Reference: AS0697). Copies may be obtained through The Mangaging Editor, International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England.

Electron diffraction techniques, Vol. II, edited by J. M. Cowley. Oxford University Press and The International Union of Crystallography, Oxford, UK, 1993, 423 pp, $70,00

Microscopy Research and TechniqueVolume 28, Issue 1 p. 79-79 Book Review Electron diffraction techniques, Vol. II, edited by J. M. Cowley. Oxford University Press and The International Union of Crystallography, Oxford, UK, 1993, 423 pp, $70,00 R. Vincent, R. Vincent H. H. Wills Physics Laboratory, University of Bristol, Bristol, UKSearch for more papers by this author R. Vincent, R. Vincent H. H. Wills Physics Laboratory, University of Bristol, Bristol, UKSearch for more papers by this author First published: 1 May 1994 https://doi.org/10.1002/jemt.1070280113AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume28, Issue11 May 1994Pages 79-79 RelatedInformation

Standardisation of polytype suffixes

The Commission on New Minerals and Mineral Names (CNMMN) of the International Mineralogical Association has published guidelines on a number of matters dealing with mineralogical nomenclature, including polytype nomenclature (e.g. Nickel and Mandarino, 1987). In essence, polytypes are distinguished by alphanumeric symbols appended to the root name and joined to it by a hyphen. The numeric part of the symbol represents the layering periodicity, and the alphabetic part, rendered in italic print, represents the crystallographic system. For example, wurtzite 4H is a hexagonal wurtzite polytype with a periodicity of 4 times the c-dimension of the wurtzite parent. Prior to the publication of these guidelines, various other polytype symbols had been used in the mineralogical literature and, in an effort to standardise polytype nomenclature, members of the CNMMN decided that previous usage should be brought into conformity with current practice, which follows recommendations of the International Union of Crystallography (Guinier et al., 1984). Polytype names in the literature that require changing are as follows:

Electron diffraction techniques, vol. I, edited by J.M. Cowley, Oxford University Press and the International Union of Crystallography, Oxford, UK, 1992, 584 pp, $85.00

Electron diffraction techniques, vol. I, edited by J.M. Cowley, Oxford University Press and the International Union of Crystallography, Oxford, UK, 1992, 584 pp, $85.00

A chloride of a substituted heterocyclic analogue of chrysene: C19H17N2O+.Cl−

thermal parameters for the H atoms were fixed throughout all subsequent refinements. Least-squares refinement converged to final R = 0.044, wR = 0.048, S = 1.416. At this point all subsequent shifts were found to be < 0.001tr. A single prominent peak is evident on the difference electron density map measuring 0.67 e A -3 in the immediate vicinity of Br. Otherwise, all remaining difference peaks were found to be < 0.39 e A -3. Anomalous scattering of Br anti S atoms was employed for verification of the proper choice of enantiomeric configuration, following the statistical criterion proposed by Hamilton (1965). The opposite enantiomorph refined to final reliability indices of R = 0.051, wR = 0.057. Scattering factors for neutral atoms and anomalous-scattering parameters for Br and S atoms were taken from International Tables for X-ray Crystallography (1974, Vol. IV). All calculations were performed on a PDP 11/60 utilizing the SDP-Plus package (Frenz, 1978). Discussion. Refined positional parameters for all atoms and equivalent isotropic B values are supplied in Table 1. Atom numbering follows the scheme indicated in Fig. 1. Fig. 2 shows a stereo OR TEP (Johnson, 1976) representation of the molecule. Interatomic bonding distances and angles are supplied in Table 2.* Bond distances and angles are, generally, as expected. The one exception to this is * Lists of structure factors, complete bond distances and angles, and anisotropic thermal parameters have been deposited with the British Library Document Supply Centre as Supplementary Publication No. SUP 55634 (18 pp.). Copies may be obtained through The Technical Editor, International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England. [CIF reference: CRI012]

Fundamentals of Crystallography. International Union of Crystallography, Oxford Univ. Press 1992, 654 p. Pb. £ 27.50. ISBN 0‐19‐855578‐4

Crystal Research and TechnologyVolume 28, Issue 3 p. 370-370 Book Review Fundamentals of Crystallography. International Union of Crystallography, Oxford Univ. Press 1992, 654 p. Pb. £ 27.50. ISBN 0-19-855578-4 C. Giacovazzo, C. GiacovazzoSearch for more papers by this authorH. L. Monaco, H. L. MonacoSearch for more papers by this authorD. Viterbo, D. ViterboSearch for more papers by this authorF. Scordari, F. ScordariSearch for more papers by this authorG. Gilli, G. GilliSearch for more papers by this authorG. Zanotti, G. ZanottiSearch for more papers by this authorM. Catti, M. CattiSearch for more papers by this authorC. Giacovazzo, C. GiacovazzoSearch for more papers by this authorP. Paufler, P. PauflerSearch for more papers by this author C. Giacovazzo, C. GiacovazzoSearch for more papers by this authorH. L. Monaco, H. L. MonacoSearch for more papers by this authorD. Viterbo, D. ViterboSearch for more papers by this authorF. Scordari, F. ScordariSearch for more papers by this authorG. Gilli, G. GilliSearch for more papers by this authorG. Zanotti, G. ZanottiSearch for more papers by this authorM. Catti, M. CattiSearch for more papers by this authorC. Giacovazzo, C. GiacovazzoSearch for more papers by this authorP. Paufler, P. PauflerSearch for more papers by this author First published: 1993 https://doi.org/10.1002/crat.2170280318AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume28, Issue31993Pages 370-370 RelatedInformation

Electron Diffraction Techniques (Volume 1). IUCr Monographs on Crystallography 3. International Union of Crystallography, Oxford University Press: Oxford 1992; 584 Seiten, ISBN 0‐19‐855558‐X. Preis £ 45.00

Crystal Research and TechnologyVolume 28, Issue 4 p. 560-560 Book Review Electron Diffraction Techniques (Volume 1). IUCr Monographs on Crystallography 3. International Union of Crystallography, Oxford University Press: Oxford 1992; 584 Seiten, ISBN 0-19-855558-X. Preis £ 45.00 J. M. Cowley, J. M. CowleySearch for more papers by this authorJ. Heydenreich, J. HeydenreichSearch for more papers by this author J. M. Cowley, J. M. CowleySearch for more papers by this authorJ. Heydenreich, J. HeydenreichSearch for more papers by this author First published: 1993 https://doi.org/10.1002/crat.2170280426Citations: 1AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article.Citing Literature Volume28, Issue41993Pages 560-560 RelatedInformation

The crystallographic information file (CIF): a new standard archive file for crystallography

The specification of a new standard Crystallographic Information File (CIF) is described. Its development is based on the Self-Defining Text Archive and Retrieval (STAR) procedure [Hall (1991). J. Chem. Inf. Comput. Sci. 31, 326-333]. The CIF is a general, flexible and easily extensible free-format archive file; it is human and machine readable and can be edited by a simple text editor. The CIF is designed for the electronic transmission of crystallographic data between individual laboratories, journals and databases: it has been adopted by the International Union of Crystallography as the recommended medium for this purpose. The file consists of data names and data items, together with a loop facility for repeated items. The data names, constructed hierarchically so as to form data categories, are self-descriptive within a 32-character limit. The sorted list of data names, together with their precise definitions, constitutes the CIF Dictionary (Core Version 1991). The CIF Core Dictionary is presented in full and covers the fundamental and most commonly used data items relevant to crystal structure analysis. The Dictionary is also available as an electronic file suitable for CIF computer applications. Future extensions to the Dictionary will include data items used in more specialized areas of crystallography.

Commission on crystal growth and characterization of materials of the international union of crystallography

Commission on crystal growth and characterization of materials of the international union of crystallography