IUCr 1999 Triennial Report - Commission on Journals

In the last triennium a number of developments for the IUCr journals should be highlighted. In the triennium the 50th Anniversary of Acta Crystallographica and the IUCr occurred, as did the 30th Anniversary of the Journal of Applied Crystallography. A special 50th Anniversary Issue of Acta Crystallographica was published in Section A in November 1998, comprising especially commissioned articles. The Guest Editor was H. Schenk whose excellent work and contribution is acknowledged here. This special issue was distributed to all subscribers of IUCr journals free of charge and is available for purchase at a very competitive price in book form. Authors' choice within the IUCr journals is broad, encompassing all aspects of crystallography and its cognate subjects across the sciences. The further expansion into the synchrotron field has been greatly facilitated by the Journal of Synchrotron Radiation, which has published the major proceedings from SRI '97 held in Himeji, Japan, and also the XAFS X Conference held in Chicago, USA, in 1998. The biological community expands apace and Acta Cryst. Section D (Biological Crystallography) is now published monthly. Publication of the very popular Daresbury CCP4 Conference Proceedings series commenced as a supplement to Acta Cryst. Section D in 1998. Chemical crystallography capability has also greatly expanded and to handle this all crystal structure data for publication in Acta Cryst. Sections B and C are now submitted electronically in the Crystallographic Information File (CIF) format. The Journal of Applied Crystallography has continued as a very successful publication and a new section on cryo-techniques is proving popular.

The IUCr web coverage of the journals, including the services to authors and Co-editors for manuscript tracking, is extensive. A 50-year searchable index has been introduced and this is a powerful tool for accessing the vast archive of IUCr publications. Most recently, proofs have been made available electronically to authors. Preparation for web access to the journals themselves is most advanced for Acta Cryst. Section D and release is imminent at the time of writing. The upcoming triennium includes an expansion of this electronic access for subscribers to the IUCr's journals.

There is a greater emphasis on the marketing of the journals to the crystallographic community, as well as to structural science communities in biology, chemistry, materials science and physics. Highlighting via mini-reviews of IUCr journal articles within the IUCr Newsletter has commenced. This opens a channel to 15,000 readers and is clearly an exciting promotional strategy. Details of each journal can be found in the accompanying reports below.

At the end of this triennium we say farewell to Section C Editor S.R. Hall who has steered Section C firmly and effectively into the electronic era, spearheading developments adopted now by various other structural chemistry and physics based journals. Also, A.M. Glazer has kept the Journal of Applied Crystallography at the forefront of experimental techniques, and launched various new sections in the journal. They are warmly wished an enjoyable and well earned respite from their heavy workloads.

In the triennium 1996—1998, Section A has published 18 bimonthly issues and a Special Issue dedicated to the 50th Anniversary of Acta Crystallographica and the IUCr. The total number of pages was 2,922, corresponding to 227 Research Papers, 3 Lead Articles, 2 Topical Reviews, 26 papers in the Special Issue, and 32 Short Communications. The number of pages and of papers published in 1997 was low, but picked up again in 1998. Many efforts have been devoted successfully at every stage to reduce the processing and printing times. The average review time is down to about four months. Efforts will continue to be made to address this crucial issue.

A highlight of the year 1998 was the Special Issue celebrating the 50th Anniversary of Acta Crystallographica and the IUCr. Its Guest Editor was H. Schenk. The Special Issue starts with a paper about the history of the IUCr and spans all aspects of crystallography, symmetrical, structural, physical, chemical and biological, with papers devoted to the most important landmarks in the development of crystallography over the past 50 years. It has also been printed as a book, under the title Crystallography Across the Sciences. This Special Issue is undoubtedly a success and more are planned. More Lead Articles and Topical Reviews are also in the pipeline.

The format of Section A seems well adapted to its purpose and no suggestions to modify it have been received in the past, but any suggestion for modification and improvement will be welcome.

In the triennium 1996—98, Section B has published 3,066 pages, comprising 335 full Research Papers, 16 Short Communications and 3 Topical Reviews (with more in the pipeline). The chemical balance of these papers is ca 45% dealing with inorganic materials, 15% dealing with metal-organics and 40% dealing with organics. Apart from papers reporting structural studies from this broad chemical spectrum, Section B continues to serve the needs of those working on charge density studies, structural systematics from the inorganic and small-molecule databases, the modelling and prediction of crystal structures, powder diffraction methodologies, studies of phase transitions, etc. The quantity of review material carried by Section B has been lower than expected. However, the value of this material lies in its quality, and it is no easy matter to secure authoritative material of this kind. Following a slight downturn in papers at the beginning of the previous triennium, coincident with the launch of Section D and the loss of biologically oriented papers, Section B has now recovered its normal average output of 1,000+ pages per annum.

Technically, Section B has come a long way during the period. CIF submission has become mandatory for structural papers, many other papers are received in machine-readable form, and in-house typesetting at the Chester office has been introduced. This latter project caused the first two issues of 1998 to be smaller than usual (ca 10 papers each), but later issues in that year soon returned to the norm of more than 20 papers per issue.

In 1997, procedures were set in place to reduce publication times. A major component of the longer publication times has been the time taken by authors to revise manuscripts in light of referee comments. This time has now been reduced to a maximum of three months, with most authors revising in much shorter times than this. Now that the in-house typesetting is in place, we would expect to see shorter publication times from 1999 onwards.

Impact statistics show that Section B remains fourth of seventeen current crystallography journals, just behind three other IUCr publications. A 'citation half-life' of more than 10 years reflects the lasting value of Section B papers.

A number of important changes have been made to the editorial and publication procedures of Section C during this triennium. Most have flowed from decisions made at the Commission meetings at the Seattle Congress in response to a rapid expansion in journal page numbers and significantly increased publication costs. The decisions spawned a number of initiatives which are intended to make the publication of structural studies more efficient for authors and the journal.

In 1997 a new electronic publication mode, known as CIF-access, was introduced. This provides for the fast, minimum-text, publication of structure determinations. The CIF-access paper is not printed but its title, scheme and synopsis appear in the Contents page of the journal in the month that the submitted material is deposited in the IUCr CIF archive. A CIF-access submission is checked identically to a full paper except that the text entries remain the responsibility of the authors. In 1998 seventy six CIF-access papers were published.

In Seattle the Section C board decided that specific quality standards were needed to promote consistent acceptance criteria for structural data, and to provide explicit author guidelines on the submission requirements. These criteria were introduced into the 1997 Notes for Authors, and became the basis for CIF checking within the Chester office. They have remained essentially unchanged over the triennium and are largely responsible for the higher quality of papers currently being published by the journal.

Another change instituted in 1997 was the removal of the atomic coordinate/anisotropic displacement parameter tables from the printed paper, except in special cases. This reduction in printed structural data was possible because archived CIFs can now easily be accessed via the IUCr web site, and this approach is more efficient and reliable as a source of structural parameters than the printed page. The recent availability of software which can be linked to the web browser means that published structures may be easily down-loaded, examined and manipulated, with a few mouse clicks. These and other web services are, as planned, providing new approaches to examining published structures, and are certain to influence the future publication directions of Section C.

The most recent change to Section C operations has been the introduction of a comprehensive suite of automatic validation and checking tests. These are used in the Chester office and as part of the, now mandatory, CHECKCIF facility. These tests are accessible via e-mail or the web. The algorithms used in this checking suite are based primarily on the criteria defined in the 1997 Notes for Authors, with the addition of 'alert level' messages to indicate the degree of departure from the expected standard. The requirement that authors pre-check their CIFs prior to submission using CHECKCIF has meant that less time and effort is wasted by authors and editorial staff on faulty submissions. In addition, authors now receive much more detailed information about the review expectations of the journal. If the author believes that any of the reported error alerts are inappropriate for a particular study, this can be explained in a supplied electronic form, known as the Validation Response Form (VRF). The VRF is, if need be, inserted into the CIF submitted for publication, and the explanations are assessed and handled by a special

Co-editor prior to the normal review step. The automatic checks have effectively shifted the emphasis of data validation and checking from the editorial office to the author, and this is of long term importance to the efficiency of the journal, and to knowledge within the discipline.

The changes to Section C in this triennium represent the transition to faster, more efficient publication modes for delivering structural information, and ensure a consistently high standard of publication through explicit acceptance criteria. The magnitude and speed of these changes has certainly stimulated some authors and, not unexpectedly, been more difficult for others. As expected of an IUCr journal, these efforts are pioneering future approaches to structural publications. This has involved a considerable effort on the part of the Chester office staff and the members of the Section C board. Their large contributions are most gratefully acknowledged.

Section D, devoted to biological crystallography, started in 1993 as a publication that appeared every other month. Since January 1999 it has appeared monthly. It contains Fast Communications, Topical Reviews, Research Papers, Short Communications, Crystallization Papers, Book Reviews and Letters. In addition, the Proceedings of the CCP4 Study Weekend, January 1998, entitled 'Databases for Macromolecular Crystallographers' was published as Part 1 of the November 1998 issue. Articles on results of crystallization experiments continue to provide important and useful information on macromolecules under study. In order to be published in Section D, deposition of all crystallographic data on biological structures (atomic coordinates and structure factors) at the Protein Databank is required. This deposition is generally as mmCIF files, so that data are available for re-refinement if needed. Publication of figures in colour is provided free of charge, but only when the colour adds to the scientific content of the article. In addition, all authors are asked to sign a form attesting to the fact that they have seen the final manuscript; this is done to obviate some problems that have occurred in the past. I thank J.R. Helliwell, the Editor-in Chief, and P.R. Strickland, the Managing Editor, for their continued support and advice through the last few years.

The subjects of research papers have included structures of a wide variety of proteins and nucleic acids. Of these, many interesting structures reported were those of a channel-forming integral membrane protein and an enzyme containing a transition-state structure in the active site. New structures, refinements of structures already known, structures of enzymes from different biological sources with somewhat different modes of action, structures as large as those of viruses, nucleosomes and ribosomes, were all reported in this journal. Details of intermolecular associations, including hydrogen bonding between water and aromatic groups, were also analysed.

The methods used to obtain such interesting structures were reported, with several articles that addressed the experimental problems encountered, how to overcome them, and discussion of the credence that should be given to the three-dimensional information that results. Subjects of articles included techniques for cryogenic data collection, methods of analysis of diffraction patterns, synchrotron data collection, X-ray structure analyses combined with electron microscopy, and the use of krypton and xenon as heavy atoms in proteins. Problems with twinning and the assignment of space group were also discussed. Crystal structures of macromolecules and their complexes are now being reported at 1.2 to 1.4 Å resolution, so that anisotropic displacement parameters and ordering of side chains at low temperatures can be evaluated. Those articles involving crystallization research addressed heterogeneity effects, descriptions of imperfections in protein crystals, comparisons of crystal growth in magnetic fields and in space and on earth, and the use of isothermal microcalorimetry, dynamic light scattering, NMR and Raman spectroscopy to study nucleation, orientational disorder, the mode of breakdown of protein crystals on melting and the structural effects of flash freezing of a crystal. Macromolecular crystal growth kinetics and morphology and the formation of polymorphs were also analysed. Articles describing methods of phasing the diffraction data involved multiple wavelength anomalous scattering with a variety of scatterers in the crystal, the various methods of density modification, phase improvement, and error estimates in macromolecular structure determinations. Molecular replacement was the subject of many articles, and it was shown that similar proteins need not necessarily associate in the same way. Patterson and real-space methods of structure determination were also addressed. Triplet phases from three-beam diffraction have been used to initiate direct methods for high-resolution protein data. Refinements of many macromolecular structures provided a more detailed picture of the atomic arrangement and the molecular folding, and several articles addressed ways of determining the reliability of a protein structure determination. Pitfalls and cautionary tales on these methods will be helpful to others with problems solving their structures.

The focus on crystallographic databases that was provided by the CCP4 Proceedings comes at a time when there is particular interest in this subject as a result of the general use of the web. Those databases of protein and nucleic acid structures, currently in place, were described together with other available databases, including those of structural motifs, intermolecular contacts and protein sequence alignment techniques. The organisers, J. Murray-Rust, L. Potterton, B. Luisi, E. Dodson and S. Bailey, are to be thanked for a highly useful publication. Previous proceedings of CCP4 study weekends have been published as Daresbury Laboratory technical reports, but it was felt that Section D would reach a wider audience.

Our sincere thanks to the many members of the crystallographic community who have served as reviewers of submitted papers. The staff at Chester have done an excellent job in shepherding the articles to the publishers, and they are also thanked. The Co-editors are also deserving of our thanks; they oversee the publication fate of a large proportion of the submitted manuscripts. Without their careful work the expansion of the journal to a monthly issue in 1999 would not have been possible.

An analysis of the contents of the Journal of Applied Crystallography over the last triennium is presented below:

Note that in 1997, the first numbers under Pages and Research Papers refer to the Special Issue containing papers presented at the Small-Angle Scattering Conference held in Campinas, Brazil. Publication of this Special Issue resulted in a slowing down of the normal publication cycle, but this matter has now been addressed, so that new arrangements for the publication of Special Issues should not interfere seriously with the normal journal production.

Even excluding the Small-Angle Scattering issue, certain healthy trends are apparent. In particular, there has been a steady growth in the number of pages published, most obviously seen in the increase in normal Research Papers. This is clearly a good situation for a journal in the present climate where electronic publication may be seen as a possible threat to paper publishing. It is gratifying also to see that the new Cryocrystallography section has shown signs of becoming popular, especially in the most recent year. Similarly the new Teaching and Education section is looking like it will be a valuable part of the journal in the future. It is also apparent that the Journal of Applied Crystallography remains the most significant of the IUCr journals carrying details about crystallographic software, although it has to be said that the Software Reviews section has been disappointing, and will need further consideration.

It is now more than four years since the Journal of Synchrotron Radiation (JSR) was launched. In this time approximately 500 research articles in over 2,400 pages have been published, providing a focus for the whole of the synchrotron radiation community. The number of papers published in JSR over the triennium has steadily increased. For the journal, the main achievement of the triennium was the successful publication of the SRI '97 Proceedings, the largest ever undertaken by the IUCr journals team, comprising over 1,050 pages. The papers for that issue were refereed to the usual JSR standards, rather than at the meeting, and we believe that this effort is reflected in the improved quality of the Proceedings over those published previously. The SRI '97 Proceedings formed the May 1998 issue of JSR. Many of the lessons learnt with SRI '97 were applied to the Proceedings of the XAFS X Meeting, held in Chicago, USA, August 1998, which is to be published in May 1999. This was again fully refereed but was produced in camera-ready format.

We have entered into the citation ranking tables and are already ranked third out of thirty seven journals covering instruments and instrumentation with Review of Scientific Instruments placed fifth, NIMS B placed sixth and NIMS A placed eighth. The review and production times for the journal have been rapid. Centralised submission was introduced in 1997 and is being used to improve review times; our current strategy is to cut production times by increasing electronification of the journal. We are currently putting together a Synchrotron Radiation and Structural Biology Special Issue (July 1999 issue of JSR) to celebrate J. Walker's (now Sir John Walker) share in the 1997 Nobel Prize in Chemistry, which is indeed the first synchrotron-radiation-related Nobel prize. Overall, the high impact factor for the journal and its excellent review and publication turn-around times for authors are fine achievements, indeed making us the best journal for the synchrotron radiation community's papers in synchrotron radiation instrumentation, methods and applications.

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