Online 28 January 2012
Notes for authors 2012
Keywords: Notes for authors.
Acta Crystallographica Section F aims to respond to the need for rapid communication in crystallization and structural biology. The journal is electronic only, articles will be published online as soon as they are ready, and a streamlined route from database deposition to publication is provided.
Structures determined through structural genomics initiatives or from iterative studies such as those used in the pharmaceutical industry are particularly welcomed by the journal.
All communications benefit from unlimited free use of colour illustrations. The Editors are also keen to encourage articles with extended multimedia capabilities and these can be submitted in any of the following categories.
Contributions should conform to the general editorial style of the journal. To take best advantage of rapid publication, communications should not exceed three journal pages (about 2000 words) and structural communications should describe a single structure. Typical articles may be viewed by going to http://journals.iucr.org/f/sample_issue.html .
These articles describe the determination of biological structures. This category provides rapid reporting of results including those from structural genomics research. Structures of protein ligand complexes or of nucleic acids are also suitable for this category. Details of data requirements for structural communications can be found at http://journals.iucr.org/f/services/structuralcommunications/ . Templates are available for this type of article (see §13.1).
Crystallization Communications should describe a coherent piece of work covering expression, purification and crystallization of a macromolecule, and the validation of crystal quality including a presentation of the diffraction data statistics. Authors should also take into account the evaluation criteria given at http://journals.iucr.org/f/services/crystallization/ . If the structure of the macromolecule has been solved already, the PDB code and any publication references should be included in the article. Templates are available for this type of article (see §13.1).
These are brief descriptions of special methods, equipment modifications, techniques for accomplishing certain tasks etc. and can be related to crystallization or other fields of structural biology.
These may deal with any aspect of crystallography, its role, its propagation or the proper function of its Societies etc. They may also deal with a technical or scientific observation that would usefully be brought to a wider audience. Letters should be submitted to one of the Section Editors or to the Editor-in-chief of IUCr Journals.
Comments of general scientific interest to the readership are welcomed. These should not normally exceed two journal pages and should be submitted as in §3.
These are short articles describing additions to, comments on, or errata to existing Section F publications and are not intended for reports of work in progress. Addenda and errata should be submitted to the Co-editor of the original article.
Articles must be submitted electronically via the web at http://journals.iucr.org/f/services/submitbdy.html or via publBio .
Full details of the submission procedure can be found at http://journals.iucr.org/f/services/submitbdy.html . Full instructions for submitting an article and details of the files required are given at http://journals.iucr.org/f/services/submitinstructions.html . Authors are encouraged to use the publBio publication tool available at http://publbio.iucr.org/ to prepare and submit their article. Authors of structural articles are required to provide a validation report on submission. Articles will be checked for plagiarism using the CrossCheck service.
Acta Crystallographica Section F will publish articles in English, French, German and Russian.
Articles should be clearly written and grammatically correct. If the Co-editor concludes that language problems would place an undue burden on the referees, the manuscript may be returned to the authors without review. Details of language-editing services can be found at http://journals.iucr.org/services/languageservices.html .
All contributions will be seen by referees (normally two) before they can be accepted for publication. The editor to whom the manuscript is assigned is responsible for the review process and for accepting or rejecting the article. This responsibility includes decisions on the final form of the article and interpretation of these Notes when necessary.
If changes to a manuscript requested by the Editor, Co-editor or the editorial staff are not received within one month of transmittal to the author, the submission will be considered as withdrawn. Should the manuscript require further revision, this would normally be expected to be completed within one month of the revision having been requested. If a manuscript is not acceptable after two revisions it will not be considered further. Any subsequent communication of the material will be treated as a new submission in the editorial process. An article that has been rejected must not be resubmitted to any IUCr journal unless the reasons given for the rejection have been fully addressed in the revised version.
For accepted articles, it is the responsibility of the Managing Editor to prepare the article for publication. This may involve correspondence with the authors and/or the responsible editor in order to resolve ambiguities or to obtain satisfactory figures or tables. The date of acceptance that will appear on the published article is the date on which the Managing Editor receives the last item required. Correspondence will be sent to the author who submitted the article unless the Managing Editor is informed of some other suitable arrangement.
Articles will be made available on the web as soon as they are ready for publication. They will receive an online publication date when they appear, and each month new online articles will be collected and published as the next issue.
On rare occasions, an editor may consider that an article is better suited to a section of Acta Crystallographica other than that specified by the author(s), to the Journal of Applied Crystallography or to the Journal of Synchrotron Radiation. Any change to the section or journal of publication will only be made after full discussion with the contact author.
The submission of an article is taken as an implicit guarantee that the work is original, that it is the author(s) own work, that all authors are aware of and concur with the submission, that all workers involved in the study are listed as authors or given proper credit in the acknowledgements, that the manuscript has not already been published (in any language or medium), and that it is not being considered and will not be offered elsewhere while under consideration for an IUCr journal. The inclusion of material in an informal publication, e.g. a preprint server or a newsletter, does not preclude publication in an IUCr journal.
The co-authors of an article should be all those persons who have made significant scientific contributions to the work reported, including the ideas and their execution, and who share responsibility and accountability for the results. Other contributions should be indicated in the acknowledgments. Changes to the list of authors will normally require the agreement of the editor and all authors.
Important considerations related to publication have been given in the ethical guidelines published in Acc. Chem. Res. (2002), 35, 74-76 and Graf et al. [Int. J. Clin. Pract. (2007), 61(Suppl. 152), 1-26 ]. Authors are expected to comply with these guidelines.
Except as required otherwise by national laws, an author must sign and submit a copy of the Transfer of Copyright Agreement form for each manuscript before it can be accepted. Authors will be asked to transfer copyright during the electronic submission process. Details of author rights can be found at http://journals.iucr.org/services/authorrights.html . See §13.4 for information on the licensing of open-access articles.
An author who believes that an article has been unjustifiably treated by the Co-editor may appeal initially to the Section Editors for a new review and, finally, to the Editor-in-chief of Acta Crystallographica if the author is still aggrieved by the decision. The initial appeal must be made within three months of rejection of the article. The decision of the Editor-in-chief is final. Any resubmission to another Co-editor will be forwarded to the Section Editors.
The contact author must provide an e-mail address for editorial communications and despatch of electronic proofs.
The source files required for an article are: a single file in Word, OpenOffice or format of the text, tables and figure captions of the article; a high-resolution graphics file (minimum 600 d.p.i.) in TIFF, PostScript or encapsulated PostScript format for each figure and scheme; and files of any supplementary material. These should be uploaded as described in the online submission instructions . Alternatively, authors may use the new version of publBio to prepare and submit their article directly.
Before preparing articles, authors should consult a current issue of the journal to make themselves familiar with the general format, such as the use of headings, layout of tables and citation of references. A sample issue is also available at http://journals.iucr.org/f/sample_issue.html .
The title should be concise but informative. Articles should also be headed by the authors' names and by the name and full postal address of the institution(s) where the work was carried out.
All contributions must be accompanied by an English language Abstract and a one or two sentence Synopsis of the main findings of the article for inclusion in the Table of Contents for the relevant issue. The Abstract should state as specifically and as quantitatively as possible the principal results obtained.
The Abstract should be suitable for reproduction by abstracting services without change in wording. It should not repeat information given in the title. Ordinarily 100 words suffice. It should make no reference to tables, diagrams, atom numbers or formulae contained in the article. It should not contain footnotes. Numerical information given in the Abstract should not be repeated in the text. It should not include the use of `we' or `I'.
Literature references in an Abstract are discouraged. If a reference is unavoidable, it should be sufficiently full within the Abstract for unambiguous identification, e.g. [Terwilliger (1994). Acta Cryst. D50, 17-23].
The main body of the article should normally be divided into the following sections: introduction; experimental, including materials and methods; results; discussion; acknowledgements; references; and tables and figures.
A set of guidelines for preparing figures is available from http://journals.iucr.org/f/services/help/artwork/guide.html . Figures should be prepared using one of the file formats listed in §3.9.
The choice of figures should be optimized to produce the shortest article consistent with clarity. Duplicate presentation of the same information in both figures and tables is to be avoided, as is redundancy with the text. Supplementary figures may be deposited (see §12).
An illustration for the first page of the article and the contents pages may be included.
Diagrams will normally be sized so that the greatest width including lettering is less than the width of a column in the journal (8.8 cm).
Fine-scale details and lettering must be large enough to be clearly legible (ideally 1.5-3 mm in height) after the whole diagram has been reduced to one column width.
Lettering should be kept to a minimum; descriptive matter should be placed in the caption.
Diagrams should be numbered in a single series in the order in which they are referred to in the text. A list of figure captions should be included in the manuscript.
Atom labelling when included should be on both left and right views in stereo perspective. Both views should be incorporated into a single figure.
Figures in colour are accepted at no cost to the author. Authors preparing colour figures should consider how the figure would look in greyscale and to readers who are colour-blind. It is very important that poor contrast (e.g. pale colours with a white background) be avoided.
The cover figure is normally a three-dimensional rotating structure. Authors who supply an mmCIF with their submission and/or use the interactive tool in described in §5.8 will be eligible for their structure to be considered for the cover.
An online tool for authors to prepare standard and corresponding three-dimensional interactive structural diagrams is available from http://submission.iucr.org/jtkt .
Extensive numerical information is generally most economically presented in tables. Text and diagrams should not be redundant with the tables.
Tables should be numbered in a single series of arabic numerals in the order in which they are referred to in the text. They should be provided with a caption.
Tables should be carefully designed to occupy a minimum of space consistent with clarity.
Each Crystallization or Structural Communication will normally include a standard experimental details table. Authors are advised to use publBio to generate this table. The tool and an example table can be found at http://publbio.iucr.org . Alternatively, a standard experimental table may be generated using the table tools option within the Word template available from http://journals.iucr.org/services/docxtemplate/ .
Authors submitting in Word should use the Word equation editor to prepare displayed mathematical equations.
The use of the stop (period) to denote multiplication should be avoided except in scalar products. Generally no sign is required but, when one is, a multiplication sign (×) should be used.
Scalar variables and non-standard functions should appear in italic type.
Vectors should be in bold type and tensors should be in bold-italic type.
Greek letters should not be spelled out.
Care should be taken not to cause confusion by using the same letter symbol in two different meanings.
Gothic, script or other unusual lettering should be avoided. Another typeface may be substituted if that used by the author is not readily available.
All displayed equations, including those in published Appendices, should be numbered in a single series.
Authors should follow the general recommendations produced by the IUCr Commission on Crystallographic Nomenclature (see reports at http://www.iucr.org/iucr/commissions/cnom.html ). Quality indicators should be given as defined in H. M. Einspahr & M. S. Weiss (2011). International Tables for Crystallography, Vol. F, ch. 2.2, pp. 64-74.
Formulae and nomenclature should conform to the rules of nomenclature established by the International Union of Pure and Applied Chemistry (IUPAC ), the International Union of Biochemistry and Molecular Biology (IUBMB ) and other appropriate bodies. As far as possible the crystallographic nomenclature should correspond to the systematic name.
References to published work must be indicated by giving the authors' names followed immediately by the year of publication, e.g. Neder & Schulz (1998) or (Neder & Schulz, 1998). Where there are three or more authors the reference in the text should be indicated in the form Smith et al. (1998) or (Smith et al., 1998) etc.
In the reference list, entries for journals [abbreviated in the style of Chemical Abstracts (the abbreviations Acta Cryst., J. Appl. Cryst. and J. Synchrotron Rad. are exceptions)], books, multi-author books, computer programs and personal communications should be arranged alphabetically and conform with the following style:
Brünger, A. T. (1992a). X-PLOR. Version 3.1. A System for X-ray Crystallography and NMR. Yale University, Connecticut, USA.
Brünger, A. T. (1992b). Nature (London), 355, 472-474.
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Acta Cryst. D54, 905-921.
Crowther, R. A. (1972). The Molecular Replacement Method, edited by M. G. Rossmann, pp. 173-178. New York: Gordon and Breach.
International Union of Crystallography (2008). (IUCr) Structural Biology and Crystallization Communications, http://journals.iucr.org/f/journalhomepage.html.
Jones, A. B. (2012). Acta Cryst. F68. In the press.
Schomaker, V. (1946). Personal communication.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
Weiss, M. S., Einspahr, H., Baker, E. N., Dauter, Z., Kaysser-Pyzalla, A., Kostorz, G. & Larsen, S. (2010). Acta Cryst. F66, doi:10.1107/S1744309110041825.
Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A. & Wilson, K. S. (2011). Acta Cryst. D67, 235-242.
Note that all authors and inclusive page numbers must be given.
Identification of individual structures in the article by use of database reference (identification) codes should be accompanied by a full citation of the original literature in the reference list. In such cases, the citation in the text should take the form `...the structure of amicyanin (PDB code 1aac, Cunane et al., 1996)'.
References in the journal will be linked, where possible, to the original publication and also to appropriate bibliographic databases (e.g. Medline).
Citations in supplementary material should also appear in the main body of the article.
Evaluation criteria and data recommended for inclusion in Structural Communications can be found on the web at http://journals.iucr.org/f/services/structuralcommunications/ .
A list of data recommended for inclusion in Crystallization Communications can be found on the web at http://journals.iucr.org/f/services/crystallization/ . Crystallization communications will typically contain no information about phase determination. However, if a statement is made which requires the determination of phases, the relevant statistics, such as the number of heavy-atom sites, phasing power, estimated phase error etc., in the case of experimental phasing, and some combination of initial rigid-body Rwork and Rfree, the correlation coefficient, or Z score, in the case of phasing by molecular replacement, need to be provided.
Guidelines for publication of NMR data are available from http://journals.iucr.org/services/nmr/ .
In articles reporting neutron data, preliminary nuclear density maps should not be included unless the relevant statistics of R, Rfree, correlation coefficient and error estimates are provided.
Guidelines for articles reporting structural modelling of small-angle scattering may be found at http://journals.iucr.org/services/sas/ . For articles that present experimental SAS data, the deposition of an ASCII file representing the background-corrected scattering profile(s) with errors is recommended.
Authors of structural articles are required to provide a validation report on submission. Authors are encouraged to presubmit their data to the wwPDB and obtain a validation report for their structure. Further information about validation reports can be found in the online submission instructions .
All supplementary content will either be made available together with the article via Crystallography Journals Online or by links to the appropriate structural databases.
All non-structural supplementary content, which may include:
Authors should follow the deposition recommendations of the IUCr Commission on Biological Macromolecules [Acta Cryst. (2000), D56, 2 ]. For all structural studies of macromolecules, coordinates and the related experimental data (structure-factor amplitudes/intensities) must be deposited at a member site of the Worldwide Protein Data Bank (http://www.wwpdb.org ) if a total molecular structure has been reported. Authors are encouraged to deposit their data with the wwPDB in advance of submission to the journal and to provide an mmCIF and a wwPDB validation report which will be required on submission. Further information about mmCIFs and validation reports can be found in the online submission instructions . Authors must supply the wwPDB reference codes before the article can be published and the data must be released upon publication.
For NMR structures, in addition to the coordinates, assigned chemical shifts and the restaint data used in the last round of refinement should be deposited with the wwPDB. It is recommended that the NOE peak list also be deposited.
Authors are encouraged to make arrangements for the diffraction data images for their structure to be archived and available on request.
An author services page is available at http://journals.iucr.org/f/services/authorservices.html .
A number of tools are available to help with the preparation of articles.
Word, OpenOffice and templates can be downloaded from the author services page.
Table tools within the Word template may be used to prepare experimental tables from an mmCIF file.
A toolkit for preparing enhanced figures is available at http://submission.iucr.org/jtkt .
Authors are encouraged to use the new version of publBio available at http://publbio.iucr.org . This web service provides a quick and easy route to prepare and submit an article, and helps to ensure that all items necessary for publication are included.
Authors may obtain information about the current status of their articles at http://journals.iucr.org/services/status.html .
Proofs will be provided in portable document format (pdf). The contact author will be notified by e-mail when the proofs are ready for downloading.
At the proof stage, authors will be given the opportunity to make their articles `open access ' on Crystallography Journals Online . Authors of open-access articles will not be asked to transfer copyright to the IUCr, but will instead be asked to agree to an open-access licence. This licence is identical to the Creative Commons Attribution Licence .
After publication, the contact author will be able to download the electronic reprint of the published article, free of charge.
All IUCr journals are available on the web via Crystallography Journals Online; http://journals.iucr.org/ .