CIF: the computer language of crystallography

Brown, I. D.; McMahon, Brian

doi:10.1107/s0108768102003464

Cited by 98 publications

(59 citation statements)

References 19 publications

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“…of pages published per year in Acta A, Acta B and JAC, 1969-1982. were introduced in 1991 in order to facilitate the direct transfer of text and numerical data from authors' computers to the typesetting programs in the Technical Editor's office, by use of the Crystallographic Information File (CIF), developed by Hall et al (1991) and derived from the STAR File system (see x13). The CIF had already been adopted in 1990 by the International Union of Crystallography as a file structure for the archiving and distribution of crystallographic information [for details, see Brown & McMahon (2002)]. These procedures became effective on 1 January 1992 and since that date all structural papers published in Sections B and C have had their numerical content checked in the Editorial Office and an archived CIF has been associated with each paper.…”

Section: : Creation Of Section Cmentioning

confidence: 99%

60 years of IUCr journals

Authier¹

2009

Acta Cryst Sect A

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In the 60 years since its birth in 1948, the number of journals published by the International Union of Crystallography has risen from one to eight. A brief account of the history of the forerunner of the IUCr journals, Zeitschrift für Kristallographie, is given. The context of the birth of the IUCr and the first of its journals, Acta Crystallographica, is recalled. The circumstances which led to the growth of Acta into several sections, at first A and B then, successively, C, D, E and F, and the launch of two new journals, the Journal of Applied Crystallography and the Journal of Synchrotron Radiation, are described. The transition from print‐on‐paper to electronic journals is also remembered.

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Section: : Creation Of Section Cmentioning

confidence: 99%

60 years of IUCr journals

Authier¹

2009

Acta Cryst Sect A

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“…• CIF -crystallographic information file 13 • mmCIF -macromolecular crystallographic information file 14 • CML -chemical markup language 15 • PDB -original Protein Data Bank format for macromolecular structures 16 • MDL MOL -file format created by MDL for molecular structures 17 • CBF -crystallographic binary file 18 • NeXus -a common data format for neutron and X-ray data 19 The different online databases provide tools to support the preparation, validation, and deposition of different sets of file formats.…”

Section: Background and Objectivesmentioning

confidence: 99%

Collaborative Annotation of 3D Crystallographic Models

Hunter

Henderson

Khan

2007

J. Chem. Inf. Model.

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This paper describes the AnnoCryst systema tool that was designed to enable authenticated collaborators to share online discussions about 3D crystallographic structures through the asynchronous attachment, storage, and retrieval of annotations. Annotations are personal comments, interpretations, questions, assessments, or references that can be attached to files, data, digital objects, or Web pages. The AnnoCryst system enables annotations to be attached to 3D crystallographic models retrieved from either private local repositories (e.g., Fedora) or public online databases (e.g., Protein Data Bank or Inorganic Crystal Structure Database) via a Web browser. The system uses the Jmol plugin for viewing and manipulating the 3D crystal structures but extends Jmol by providing an additional interface through which annotations can be created, attached, stored, searched, browsed, and retrieved. The annotations are stored on a standardized Web annotation server (Annotea), which has been extended to support 3D macromolecular structures. Finally, the system is embedded within a security framework that is capable of authenticating users and restricting access only to trusted colleagues.

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“…To help this maturation process, standardized practice should be established in the simulation community, similar to that in crystallography. 2,3 It is already regular practice to print quality measures in a formulaic table in published articles reporting crystallographic resultssindeed, it is surprising if such a table is missing, and the referees would readily reject the manuscript.…”

Section: Overviewmentioning

confidence: 99%

Quality Assurance for Biomolecular Simulations

Murdock

Tai

et al. 2006

J. Chem. Theory Comput.

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Abstract:Contemporary structural biology has an increased emphasis on high-throughput methods. Biomolecular simulations can add value to structural biology via the provision of dynamic information. However, at present there are no agreed measures for the quality of biomolecular simulation data. In this Letter, we suggest suitable measures for the quality assurance of molecular dynamics simulations of biomolecules. These measures are designed to be simple, fast, and general. Reporting of these measures in simulation papers should become an expected practice, analogous to the reporting of comparable quality measures in protein crystallography. We wish to solicit views and suggestions from the simulation community on methods to obtain reliability measures from molecular-dynamics trajectories. In a database which provides access to previously obtained simulationssfor example BioSimGrid (http://www.biosimgrid.org/)sthe user needs to be confident that the simulation trajectory is suitable for further investigation. This can be provided by the simulation quality measures which a user would examine prior to more extensive analyses. OVERVIEWFor the past quarter century, biomolecular simulations have been adding value to structural biology via the provision of dynamic information. 1 As genomics move from sequencing to structural and dynamical considerations, and highthroughput technologies advance from crystallography to molecular-dynamics (MD) simulation, this process is occurring with vigor. As the bibliometric data in Figure 1 show, MD simulation of biopolymers is now becoming a routine technique. To help this maturation process, standardized practice should be established in the simulation community, similar to that in crystallography.2,3 It is already regular practice to print quality measures in a formulaic table in published articles reporting crystallographic resultssindeed, it is surprising if such a table is missing, and the referees would readily reject the manuscript.We are hereby initiating a discussion on the appropriate measures of quality and convergence 4 for MD simulation trajectories of biopolymers. The process of calculating these measures is designed to be automated for large numbers of trajectories; hence the set of analyses used for this description should be general, with minimal interaction of a human curator. The scientist can then use these measures, along with sensible comparisons with known experimental data (which we recognize as essential), to decide whether a specific trajectory is suitable for further investigation. Our purpose is to solicit feedback from the simulation community with regard to the analyses we have chosen and to obtain further suggestions. We invite the community to express their views on our choices of measures.We are motivated to do this by our work in building BioSimGrid, 5 a distributed environment for archiving and analyzing biopolymer simulations. Other similar databases are emerging 6 (personal communications with Valerie Daggett and Modesto Orozco, http://mmb.pcb.u...

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CIF: the computer language of crystallography

Cited by 98 publications

References 19 publications

60 years of IUCr journals

60 years of IUCr journals

Collaborative Annotation of 3D Crystallographic Models

Quality Assurance for Biomolecular Simulations

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