EDITORIAL
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EDITORIAL Just over 3 years ago, the first Special Issue of the Journal of Structural Biology was published. Edited by Bridget Carragher and Ross Smith, its central theme was computational tools for processing electron micrographs of biological specimens. This volume has had a major impact on the field, as attested by its heavy citation pattern. In the interim, software and hardware have continued to develop and proliferate, spurred by the connectivity opportu- nities afforded by the Internet. Three years is a long time in most branches of computing, and imaging of macromolecular and cellular structures is no exception: its scope has expanded immensely over this short interval. Recogniz- ing these advances, the current editors have coordinated another Special Issue that aims to capture emerging trends in digital imaging with particular emphasis on the opportunities afforded by the Internet to share procedures and information. This issue brings together an eclectic collection of papers in which four major subthemes may be distinguished. The Protein Data Base has played a central role in collating and disseminat- ing X-ray crystallographic structures. The need for a comparable data base for microscopy was recognized in the conception of the BioImage project, a timely initiative of the European Union, led by JoseMaria Carazo and Ernst Stelzer, whose paper summarizes its overall scope. The central element of BioImage is an object-relational data base, whose design principles are presented in the article by Lindek et al. Pittet et al. describe the development of tools for handling image data in the Web environment, while de Alarco ´n et al. present a ‘‘query by content’’ approach to accessing data. Aspects of video microscopy and the handling of time-resolved images in general, a topic of large and still growing importance, particularly in structural cell biology, are addressed by Boudier and Shotton. The increasingly close and fertile synergy of cryo-electron microscopy and X-ray crystallography is the second major element of this Special Issue. Even at relatively modest resolutions, 3-D envelopes of macromolecular complexes calculated from cryo-micrographs often capture enough detail to allow the precise docking of subunits for which atomic models are available, thus allowing unique insights into intermolecular interactions. XtalView/Xfit, a new graphics package for manipulating and displaying high resolution density maps, is outlined by McRee. Belnap et al. describe procedures for converting PDB coordinate sets into low-resolution molecular envelopes suitable for integration with EM data, and Wriggers et al. and Volkmann and Hanein describe their respective approaches to automated, quantitative docking of models into maps that will surely supercede the visual interactive approach that has been used to date. Third, several papers deal with various aspects of the calculation of 3-D cryo-EM maps and analysis of their contents. Rossmann and Tao present the theoretical basis of a new method of image reconstruction that draws on crystallographers’ concepts of noncrystallographic symmetry. Casto ´n et al. present a procedure for producing reliable starting models for hard-to-solve icosahedral viruses, to be used in a model-based procedure. Ravantti and Bamford describe their approach to systematically dissecting cryo-EM density maps into sets of connected features with a view to interpreting them in Journal of Structural Biology 125, 95–96 (1999) Article ID jsbi.1999.4109, available online at http://www.idealibrary.com on 95 1047-8477/99 $30.00 Copyright r 1999 by Academic Press All rights of reproduction in any form reserved.
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Journal of Structural Biology 125, 95–96 (1999)Article ID jsbi.1999.4109, available online at http://www.idealibrary.com on
EDITORIAL
Just over 3 years ago, the first Special Issue of the Journal of StructuralBiology was published. Edited by Bridget Carragher and Ross Smith, itscentral theme was computational tools for processing electron micrographs ofbiological specimens. This volume has had a major impact on the field, asattested by its heavy citation pattern. In the interim, software and hardwarehave continued to develop and proliferate, spurred by the connectivity opportu-nities afforded by the Internet. Three years is a long time in most branches ofcomputing, and imaging of macromolecular and cellular structures is noexception: its scope has expanded immensely over this short interval. Recogniz-ing these advances, the current editors have coordinated another Special Issuethat aims to capture emerging trends in digital imaging with particularemphasis on the opportunities afforded by the Internet to share procedures andinformation. This issue brings together an eclectic collection of papers in whichfour major subthemes may be distinguished.
The Protein Data Base has played a central role in collating and disseminat-ing X-ray crystallographic structures. The need for a comparable data base formicroscopy was recognized in the conception of the BioImage project, a timelyinitiative of the European Union, led by JoseMaria Carazo and Ernst Stelzer,whose paper summarizes its overall scope. The central element of BioImage isan object-relational data base, whose design principles are presented in thearticle by Lindek et al. Pittet et al. describe the development of tools forhandling image data in the Web environment, while de Alarcon et al. present a‘‘query by content’’ approach to accessing data. Aspects of video microscopy andthe handling of time-resolved images in general, a topic of large and stillgrowing importance, particularly in structural cell biology, are addressed byBoudier and Shotton.
The increasingly close and fertile synergy of cryo-electron microscopy andX-ray crystallography is the second major element of this Special Issue. Even atrelatively modest resolutions, 3-D envelopes of macromolecular complexescalculated from cryo-micrographs often capture enough detail to allow theprecise docking of subunits for which atomic models are available, thusallowing unique insights into intermolecular interactions. XtalView/Xfit, a newgraphics package for manipulating and displaying high resolution densitymaps, is outlined by McRee. Belnap et al. describe procedures for convertingPDB coordinate sets into low-resolution molecular envelopes suitable forintegration with EM data, and Wriggers et al. and Volkmann and Haneindescribe their respective approaches to automated, quantitative docking ofmodels into maps that will surely supercede the visual interactive approachthat has been used to date.
Third, several papers deal with various aspects of the calculation of 3-Dcryo-EM maps and analysis of their contents. Rossmann and Tao present thetheoretical basis of a new method of image reconstruction that draws oncrystallographers’ concepts of noncrystallographic symmetry. Caston et al.present a procedure for producing reliable starting models for hard-to-solveicosahedral viruses, to be used in a model-based procedure. Ravantti andBamford describe their approach to systematically dissecting cryo-EM density
maps into sets of connected features with a view to interpreting them in95 1047-8477/99 $30.00Copyright r 1999 by Academic Press
All rights of reproduction in any form reserved.
96 EDITORIAL
molecular terms. Smith provides a description of Ximdisp, the image displayinteractive core of the MRC image processing package.
Fourth, the Internet not only connects interested parties with data but alsoallows remote users to operate and control imaging devices. Recent advances intelemicroscopy are addressed by Kisseberth et al. and Hadida-Hassan et al.,who discuss the strengths and limitations of this technology. Finally, Sosinskyet al. describe the ‘‘Electron Microscopy Outreach Program,’’ a Web resourceproviding access to both software and learning materials for the EM commu-nity.
The first Journal of Structural Biology Special Issue on Computational Toolsinfused major momentum to structural studies of macromolecular complexes, atrend that will surely be sustained by the current collection of articles.Extrapolating further, we anticipate a third Special Issue in this series inanother 2 years or so and invite all those who work at the cutting edge insoftware development for structural and molecular biology to bear this in mind.
And finally, we express our appreciation to the authors of all articles, to allthose who reviewed the papers of this Special Issue, and for the constructiveresponse of the authors to this rigorous scrutiny.
Ross Smith, Andreas Engel, and Alasdair Steven
