online submission instructions

The following instructions for submitting to Acta Crystallographica Section D are organized in question-and-answer format. You can read through the questions in order, or click on any of the questions to jump directly to the answer. When you are ready to continue, go back to the submissions home page.

Context sensitive help is available throughout the submission procedure by holding your mouse over underlined text in the submission forms or by clicking on the help icons [info]

Please note: These instructions should be read together with the Notes for Authors, which give overall guidelines on submitting an article.

Getting started

Submission and review

Getting help

Getting started

How do I begin submitting an article?

When you are ready to submit an article and have all the necessary items ready, you should go to the submissions home page to start the process. To submit your article, you will be asked to provide information on your submission, to upload your article and graphics files, and to select a Co-editor. The process is reasonably self-explanatory, and detailed help is provided along the way.

Back to contents

What should I have ready before starting a new submission?

Before you begin submitting, you should have the following items ready:

  • a covering letter detailing the reasons why your article is suitable for publication in Acta Crystallographica Section D;
  • your article prepared as a single file (see below for more information on files);
  • a high-resolution graphics file in TIFF, PostScript, encapsulated PostScript, JPEG, PNG or HPGL format for each figure and scheme, together with any supplementary files you wish to submit;
  • if your article reports a structure, a full wwPDB validation report, the name of your structure and the relevant supporting information (see below);
  • your full contact details (e-mail address, postal address, telephone and fax numbers);
  • details of the authors of your article (surnames, forenames and e-mail addresses of all authors);
  • other details of the article you are submitting (article title, language in which your article is written, article category);
  • an abstract in plain, unformatted text, ready to be copied and pasted (or typed directly) into the web site;
  • suggestions for referees (surnames, forenames and e-mail addresses of possible referees);
  • the location of your article file on your local filesystem.

In addition, it may be useful to have selected, in advance, Co-editors whose areas of expertise best match your article.

Back to contents

What does the overall submission and review procedure involve?

The overall procedure involves six stages:

  • Stage 1
    You will be asked to provide your e-mail details and the article title, to select your article category and state if your article reports a structure. You will also be asked to upload a single file of the text of your article. Details of the file required are given below.
  • Stage 2
    You will be asked to give further details of your article (see above). 
  • Stage 3
    You will be asked to upload high-resolution graphics files and supporting information for your article (see below). Note that you should only click on the CONTINUE button when you have uploaded all relevant files and have checked the PDF review document.
  • Stage 4
    You will be asked to choose whether to make your article open access or to agree to an IUCr licence to publish. You will also be required to state that you have complied with the ethical requirements of the journal.
  • Stage 5
    You will be asked to select a Co-editor, from a list of those available, to coordinate the review of your article. Details of possible referees should be typed into the spaces provided. A covering letter should also be supplied.
  • Stage 6
    Your submission is now complete. A PDF review document is generated from the file(s) you submit and you will be provided with a web address for accessing and viewing this document.

    Once your review document is created, the system will assign a Co-editor to your article. You will be given the contact details of this Co-editor and a Co-editor reference code. The reference code has two letters and four digits (e.g. au0165) and should be quoted in all subsequent communications with the Co-editor and the Editorial Office. You should keep a record of the web address for viewing your article and the Co-editor code of your article.

    The Co-editor will arrange for the review of your article and will inform you by e-mail of the outcome of the review. You may be asked to submit revised versions of your article (see below). Please note that revisions should only be submitted at the request of the Co-editor handling your article.
Back to contents

What special considerations are there for structural papers?

Authors of structural papers are required to presubmit their data to the Worldwide Protein Data Bank (wwPDB), and obtain a PDB deposition code. During submission they should then provide data for each reported structure, for review purposes only, as follows.

For crystal structures

  • the PDB deposition code;
  • the name of your structure;
  • a full wwwPDB validation report (see below);
  • a file containing coordinates (mmcif or pdb file);
  • a reflection data file, preferably as intensities and their estimated standard uncertainties (mmcif or mtz file);
  • authors are also encouraged to include anomalous dispersion data and/or experimental phases where appropriate.

Authors using small-angle scattering should also deposit their data with the SASBDB and provide an SASBDB deposition code.

Authors of nucleic acid structures may deposit their data with the Nucleic Acid Database (NDB) and provide an NDB deposition code.

For cryo-EM structures

  • the PDB deposition code;
  • the name of your structure;
  • a full wwwPDB validation report (see below);
  • a file containing coordinates (mmcif or pdb file);
  • map image file;
  • primary map file;
  • half maps.

Additional maps, FSC curves, intensities and layer line data may also be submitted where appropriate.

For NMR structures

  • the PDB deposition code;
  • the name of your structure;
  • a full wwwPDB validation report (see below);
  • a file containing coordinates (mmcif or pdb file);
  • restraint file(s) (mr or tbl files);
  • chemical shift file (str file);
  • authors are also encouraged to upload a peak list file.
Back to contents

Submission and review

What kinds of file may I submit?

For submission and refereeing we require the word processing and other source files for your article to be submitted. The files should be prepared according to the Notes for Authors.

You may submit either (a) WORD or OpenOffice files, or (b) LaTeX files.

WORD or OpenOffice submissions:

At Stage 1, we require a WORD or OpenOffice file of the text, tables and figures of your article to be uploaded.

At the file upload stage, you will be asked to provide the following source files:

  • A high-resolution graphics file in TIFF, PostScript, encapsulated PostScript, JPEG or PNG format for each figure and scheme
  • Files of any supporting information that cannot be included at the end of your article e.g. videos
  • Relevant supporting information (see above) for each structure reported
For each source file you will be asked to
  • Select the role of the file, its number and part number as applicable
  • Locate the file on your local system
  • Upload the file

You may overwrite an incorrectly uploaded file by uploading a replacement file with the same role, number and part number.

Once you have uploaded all your files, you should click on REGENERATE REVIEW DOCUMENT and check that the PDF review document generated by the submission system is up to date and correct. If there are no problems, you should then click CONTINUE to go to the next stage.

LaTeX submissions:

At Stage 1, we require a LaTeX file of the text, tables and figures of your article to be uploaded.

At the file upload stage, you will be asked to provide the following source files:

  • A BibTeX file (note that this file is optional, as authors may alternatively include the bibliography within the LaTeX file)
  • A high-resolution graphics file for each figure and scheme (see below for special considerations for LaTeX submissions)
  • Files of any supporting information that cannot be included at the end of your article e.g. videos
  • Relevant supporting information (see above) for each structure reported

For each source file you will be asked to

  • Select the role of the file, its number and part number as applicable
  • Locate the file on your local system
  • Upload the file

You may overwrite an incorrectly uploaded file by uploading a replacement file with the same role, number and part number.

Once you have uploaded all your files, you should click on REGENERATE REVIEW DOCUMENT and check that the PDF review document generated by the submission system is up to date and correct. If there are no problems, you should then click CONTINUE to go to the next stage.

Back to contents

Should I use a template to prepare my article?

Templates are available for the preparation of your article in WORD or LaTeX format. For review purposes, please ensure that the file you prepare is in preprint format (single column, double spaced). Graphics should be included in WORD files for review purposes.

Back to contents

How should I prepare my figures?

A set of guidelines for preparing figures is available. Figures should be prepared using one of the file formats listed above.

When uploading figures for LaTeX submissions, please upload the figure files that you used to create a valid LaTeX document on your own computer. The submission system will automatically detect their type and rename them if necessary for processing. In most cases, if you have prepared your LaTeX document for printing as PostScript, your figures will be in .ps or .eps format. If you have prepared your document for printing as PDF, the figures will usually be in .png or .pdf format.

Back to contents

Should I submit supporting information?

If your article reports a macromolecular structure determination, you will need to upload the PDB code and name of your structure, the full PDB validation report and the relevant supporting information (see above) during the submission procedure.

Other supporting information (e.g. videos) may be submitted; for a full list of allowed file types, click here.

Supporting information that is for "review only" can be uploaded in the same way as regular supporting information but it should be made clear on the first page of the material that it is for review only and not for publication.

Authors are encouraged to archive their raw diffraction data and provide digital object identifiers (DOIs) during submission for these data sets. A description of the data sets will also be requested.

Back to contents

What is a full wwPDB validation report?

When coordinates and structure factors are deposited with one of the Worldwide Protein Data Bank (wwPDB) sites a PDB validation report is created and made available to the depositor. After the entry is processed by a member of the wwPDB biocuration team, the full official confidential validation report will be sent to the depositor or can be downloaded from the web at the Validation Reports page of the wwPDB deposition interface. The relevant PDB code and the name of the structure should be given for each PDB validation report uploaded during your submission.

Back to contents

What is an mmCIF?

mmCIF stands for macromolecular Crystallographic Information File which is a plain text file format which describes a macromolecular crystallographic experiment and its results. When the coordinates and structure factors for a structure are deposited with the wwPDB an mmCIF for the structure will be created and made available to the depositor.

Back to contents

What data should I upload?

Data may be uploaded as separate files or as a zip file. One zip file should be provided for each structure and contain all the relevant files for the structure as detailed below. Files in the zip should be named using the database code for the structure they relate to and the appropriate suffix, e.g. 8abc.cif, 8abc.mtz.

For crystal structures

For each structural model, the following should be provided upon submission: the wwPDB reference code(s), a full wwPDB validation report, a file containing coordinates (mmcif or pdb format), and a reflection data file, preferably as intensities and their estimated standard uncertainties (mmcif or mtz format). Authors are also encouraged to upload anomalous dispersion data and/or experimental phases where appropriate (e.g. for metal identification).

For cryo-EM structures

For each structural model, the following should be provided during submission: an EMDB reference code, a full wwPDB validation report, molecular coordinates (mmcif or pdb file), a primary map file, a map image file. Authors are also encouraged to upload half maps, additional maps and FSC curves where appropriate.

For NMR structures

For each structural model, the following should be provided during submission: the wwPDB reference code(s); a full wwPDB validation report, molecular coordinates (mmcif or pdb file), a chemical shift file (.str), at least one restraints file (.tbl or .mr). Authors are also encouraged to upload a peak list file.

Back to contents

What do I need to do about copyright?

When the files for your article have been successfuly uploaded, you will be asked to agree to an IUCr licence to publish or alternatively to publish your article open access. You will also be required to state that you have complied with the ethical requirements of the journal. Authors selecting open access do not need to transfer copyright. Details of author rights can be found at https://journals.iucr.org/services/authorrights.html.

Back to contents

Where should I put my response to the review of my article?

You should generally respond to review comments by e-mailing the Co-editor handling your article using the contact co-editor tab on the article review page; if your article has been revised it should also be re-uploaded at this stage, see below. Short responses to review comments may be pasted or typed into the space provided at the foot of the upload revision tab.

Back to contents

How do I submit a revised article?

To upload a revised version of your article following review comments, you should use the web address supplied to you during the initial submission procedure. The Co-editor will instruct you as to which files they require to be revised. In some circumstances the Co-editor may elect to revise your article and ask you to review the revised article at the web address for your article. Revised graphics files and supporting information may also be requested at this stage. If figures need to be renumbered as a result of the revisions, use the change ordering of figures button to renumber the figures.

Please note: revisions should be submitted only at the specific request of the Co-editor handling your article.

Back to contents

Getting help

What are some common pitfalls I should avoid?

  • Make sure that you follow the specific instructions for WORD, OpenOffice and LaTeX submissions. Failure to follow the instructions may result in an incomplete review document being sent to the Co-editor.
  • Check your article fully before submitting it. If you find problems after the submission is complete, you may be required to resubmit your article online. Any such changes could delay the processing of your article.
  • Make sure you have included a covering letter with your submission.
  • Be sure to use only the supported file formats. Your submission may not be processed if you use any other formats, and you may need to resubmit it.
Back to contents

What tools are available to help prepare my article?

A number of tools are available to help with the preparation of articles:

Back to contents

What if the Co-editor I wish to submit to is unavailable?

If you have a preference for a particular Co-editor, and that Co-editor is not available when you submit your article, you should check at the Co-editor assignment stage to see when the Co-editor will next be available. (Note that if you indicate a preference for a Co-editor who is not currently available, this may delay the review of your article.) If you wish to submit a series of related papers to the same Co-editor, please contact supportd@iucr.org before starting your submissions.

Back to contents

What is an IUCr ID?

Your IUCr ID is your user name for all IUCr online services. The International Union of Crystallography has brought several of its online services for users, including the World Directory of Crystallographers and e-mail alerting for IUCr journals, under a single registration system. With this system, each user needs to register information such as their name and e-mail address only once, and can simply and easily keep their own information up to date.

If you have registered an IUCr ID, you may be able to claim a member discount on your open-access publication fees.

Find my IUCr ID

Registration is simple, with only a small amount of information required, although users who wish to be included in the World Directory of Crystallographers should provide contact and biographical information that is as complete as possible. Once registered, each user may use their IUCr ID and password at any time, for instance to log in to update their details for the World Directory of Crystallographers, or to change e-mail addresses and the e-mail alerts received at each address.

Back to contents

What should I do if I do not have the e-mail address of a co-author?

During submission you will be asked to provide e-mail addresses for all authors. These addresses will be used to inform your co-authors that the article has been submitted and may also be included in the metadata associated with the article. In some cases, e.g. where a co-author is a student who is no longer at your institution, it may be difficult to provide an e-mail address. If you are unable to find an address for a co-author, you may substitute your e-mail address.

Back to contents

What should I do if I get stuck?

You will find detailed help links [info]  throughout the submission pages, and you can use any of these links without stopping the submission. If you are having more serious problems, you should contact supportd@iucr.org.

Back to contents
Follow Acta Cryst. D
Sign up for e-alerts
E-alerts
Follow Acta Cryst. on Twitter
Twitter
Follow us on facebook
Facebook
Sign up for RSS feeds
RSS