publBio article preparation and submission instructions

Getting started

The following are instructions for preparing and submitting Research Communications to Acta Cryst. F using publBio. A video will also be available in due course.

publBio makes writing and submitting your Acta Cryst. F article easy. It guides you through the preparation of your article by including all the sections required and helps you keep to the suggested number of words. It lists all the items editors ask for in tables and can automatically fetch some of the data from your mmCIF or PDB file. It prompts you for figures and the other items needed for your article.

Once your article has been written it provides a quick and easy route to submission by bypassing many of the initial stages of the usual submission process. If you get stuck detailed help is provided along the way.

A Word template is also available for the preparation of your article. Table tools within the Word template have some of the functionality of publBio but does not support the quick route to submission offered by publBio.

How to prepare your article

To get the best out of publBio this page should be read in conjunction with the Notes for Authors and the online submission instructions.

When you are ready to prepare an article and have all the necessary items ready, you should go to http://publbio.iucr.org to start the process.

 

What to have ready before starting a new article

• if your article reports a crystal structure and you have an mmCIF for your structure, you should have this ready; alternatively if your structure has been deposited in the Protein Data Bank (and has been released) you should have the PDB code;
• a high-resolution graphics file in TIFF, PostScript or encapsulated PostScript format for each figure;
  
• your full contact details (e-mail address, mailing address, telephone and fax numbers);
• details of the authors of your article (surnames, forenames and e-mail addresses of all authors);
• if you are reporting a structure you will need the PDB code and PDB validation report for your structure;
• later in the process you will need your choice of Co-editor, suggestions for referees (surnames, forenames and e-mail addresses of possible referees)

Starting to use publBio

To use publBio you first need to register at http://publbio.iucr.org so that your articles are kept secure. Registration requires some very basic information such as name, address and e-mail address.

When you first login you go to the `My articles' page where you can start to write a new article. Once you have used publBio this page will also list the articles you are currently working on or articles that you have submitted or published already. The `My articles' button in publBio will also take you to this page.

Starting a new article

To start a new article choose one of the following options:

• Enter a PDB code in the box. Press the enter key and publBio will fetch the data for the structure (provided it is released by the PDB) and prefill some of the tables and text in the template.
• Upload an mmCIF or PDB file from your local file system. This file is then used to prefill some of the tables and text in the template.
• Fetch a PDB or mmCIF file from an internet location. This file is then used to prefill some of the tables and text in the template.
• Write an article without a data source. This will open a blank article template ready for you to enter your text, tables and figures.

Writing your article

Once publBio has retrieved your data or a blank template has been opened, your article appears in the centre of the screen. To edit your article click in the part of the article you want to work on. Clicking in some areas will make a box appear for you to enter information while in other areas you can edit text directly.

At the left of the screen there are a number of buttons for adding markup to the text such as bold, italic or adding symbols, and for saving your article. At the top there are also buttons to go to the My articles page, to save your work with another name, share the article with a colleague or print it out as a PDF file, and when your article is ready for submission you can use the `Submit to Acta F' button.

Use the `Paper options' button to choose which type of article you are going to write. If writing an article about a structure determination, you can choose if you want to include a table of crystallization details (if the crystallization details have been published before you may just want to include a reference to the crystallization communication instead).

Authors and affiliations

Clicking on the authors allows you to enter author details and affiliations, or use those from a previous author or even a previous project in publBio. If the author is in the World Directory of Crystallographers, this can be searched to obtain this author's details. Authors can be added, removed or their position in the list altered. If using publBio to submit to Acta F, the submitting and correspondence authors should be indicated, and all authors should be given an e-mail address. If an item is missing, e.g. an author's e-mail address, a warning may appear in the left-hand margin. You should attempt to fix any problems highlighted here before trying to submit your article.

Synopsis, abstract, keywords

These should be filled out as appropriate, following the suggested word limits (see below).

Text of the article

The article is split into defined sections and, for guidance, a suggested word limit is shown in the left-hand margin. There are standard main section headings and if you click on a section, guidelines for what should be included in each section will appear. Your text should be added, as indicated, in the paragraphs beneath the headings.

Tables

Clicking on a table allows you to edit the text and perform simple operations such as adding or deleting columns and rows.

If you have uploaded an mmCIF or given a PDB code for a released structure, some of the data in the tables may be prefilled directly and some data may be derived from values in the mmCIF (included underlined and in bold). All these values should be checked carefully. You will need to add values where they have not been available or provide explanations in some cases as detailed in the table footnotes. The tables list the items required for a submission so you should try to fill in as much of the information as possible and not delete any items unless there is good reason to do so.

Without an mmCIF or PDB code you will have a blank template for you to add your own data.

All tables should be called out in the text.

Figures

Clicking on a figure allows you to upload a file for your figure and other simple operations relating to figures. Figure files should be prepared according to the Notes for Authors. A set of guidelines for preparing figures is also available. Up to three figures are allowed and an example of the content of each figure required is also given. The caption should be edited to fit the figure you upload. Figures should be called out in the text as appropriate.

References

A list of references cited in the text should be included and arranged alphabetically.

Supporting information

Any extra information for your article can be uploaded in the Supporting Information section at the foot of the article. This can include experimental data, additional figures and multimedia content; for a full list of allowed file types, click here.

If your article reports a structure, you must supply the PDB/NDB deposition code, the name of your structure and a PDB validation report for each structure reported. Authors are strongly encouraged to upload the refined coordinates and the structure factor amplitudes including phases for review purposes.

Saving and viewing files

You should save your work frequently in case of internet problems and you can use the `Save as' button to rename your article.

Clicking on the `PDF' button allows you to view your article as a PDF file. When you start to submit your article a review PDF file will be generated and you should check this before you continue with the submission.

Submitting your article

When you are ready to submit press the `Submit to Acta F' button and you will be redirected the IUCr submission system. The files needed for submission will be transferred automatically to the submission system so you will not need to upload these again.

You will enter the submission system at Stage 4 and from this point the submission will be the same as if submitting without using publBio (see the online submission instructions for more details). You will be asked if you wish to transfer copyright to the IUCr or if you require your paper to made open access.

You will then be asked to choose a Co-editor and provide referee suggestions. You will also be asked to provide a covering letter and this may be pasted into the webform or uploaded as a separate file.

Revisions

When asked to revise an article, go to the web address given to you by the Co-editor. Click on the `upload revision' tab and this will take you to your publBio articles page. Open and edit your article in the usual way and when you have completed your changes you can submit your revised version using the `Submit a revision' button. At the end of the revision, please send the Co-editor a list of your revisions using the `contact co-editor' tab. Please note: revisions should be submitted only at the specific request of the Co-editor handling your article.

Further help and information

Special considerations for structural papers

Authors of structural papers are required to presubmit their data to the Protein Data Bank (PDB) and provide the PDB deposition code and a PDB validation report for each reported structure (see below). Authors are strongly encouraged to upload the refined coordinates and the structure factor amplitudes (including phases) as supporting information. These data will only be available for review purposes. Authors of nucleic acid structures should deposit their data with the Nucleic Acid Database (NDB) and provide an NDB deposition code.

PDB validation reports

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. The report is usually sent to the depositor as a PDF file or can be downloaded from the web. The PDB code and name of the structure should be given for each PDB validation report uploaded.

mmCIFs

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 RCSB PDB or PDBj an mmCIF for the structure will be created and made available to the depositor. Alternatively, if authors use the IUCr publBio annotator tool they will be able to save their data as an mmCIF. It is also possible to convert your PDB file to an mmCIF using maxit-v8.120-prod-bin available from http://sw-tools.pdb.org/ apps/MAXIT/index.html . An example of an mmCIF can be obtained by clicking here.

Using a template to prepare your article

A Word template is also available for the preparation of your article. Table tools within this template have some of the functionality of publBio but the template does not support the quick route to submission offered by publBio.

What to do about copyright

During the submission process you will be asked to either transfer copyright or choose open access for your article. Authors of open-acess articles retain copyright of their article and if you choose open access you will be asked to confirm that you agree to a Creative Commons Attribution licence for your article. Please note that you can make your article open access at any time after submission by contacting support@iucr.org. More details about making your article open access can be found here.

Choosing a Co-editor

Before you start a submission you should choose a Co-editor whose subject area most closely matches the subject of your article. If the Co-editor you have chosen is not available when you submit your article, you should check 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 supportf@iucr.org before starting your submissions.

What is an IUCr ID?

Your IUCr ID is your user name for all IUCr online services including publBio. The International Union of Crystallography has brought several of its online services for users, including publBio, 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. When using publBio you will login using your IUCr ID.

If you are already registered (e.g. if you are already in the World Directory of Crystallographers), click here to search for your IUCr ID. To avoid confusion, please do not register more than once.

What to do if you do not have the e-mail address of a co-author

For submission from within publBio you will need to provide e-mail addresses for all authors. These addresses will be used to inform your co-authors that the article has been submitted. 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 coauthor, you may substitute your e-mail address.

What to do if you get stuck

You will find detailed help links throughout publBio and the submission pages . If you are having more serious problems, you should contact supportf@iucr.org.