Crystallographic data (CIF) info for American Mineralogist

Introduction

The CIF (crystallographic information file) format is the de facto standard for communicating all sorts of crystallographic information. In particular it is used to archive crystal structure data, combined with experimental and refinement details.

Manuscripts reporting results of crystal structure refinements must be accompanied by a CIF providing the structural data. To ensure quality and integrity of the crystallographic data, the submitted CIF will be reviewed by the Am Min technical editing team. After publication of the manuscript, the CIFs will be made available as supplementary material on the Am Min webpages. They may also be deposited into databases, such as the AMCSD (American Mineralogist Crystal Structure Database) and the COD (Crystallography Open Database).

Since a CIF contains atomic fractional coordinates and displacement parameters as well as sample measurement conditions, separate tables listing these parameters are generally unnecessary. Exceptions include brief tables of crystallographic parameters (such as selected bond lengths or bond valence sums) that are central to the discussion in the paper, especially if the tables help the reader to understand the comparison of multiple structures.

Submission Guidelines

Only one CIF should be submitted with a manuscript. If more than one structure refinement is reported in a manuscript, each structure refinement must be a separate data block in the CIF. Do not compress or otherwise modify the CIF for submission. The filename extension must be '.cif'.

Detailed information about CIF requirements for manuscripts submitted to American Mineralogist, help and advice, are in the AmMinCifGuide.pdf.

Minimum CIF Requirements

The minimum requirements for a CIF submitted to American Mineralogist are, in brief:

1. It must conform to the CIF syntax as defined by the (IUCr).
2. It must contain appropriate information about composition, mineral name, and locality/source.
3. It must contain the unit cell parameters, symmetry information and space group, the fractional coordinates and displacement parameters of the atoms.
4. The experimental conditions (temperature, pressure) and basic information about the experiment (radiation, diffraction measurement type) must be reported.
5. The reported data must be physically-reasonable and crystallographically consistent.
6. It must contain all structures reported in the manuscript. Only one CIF is to be submitted per manuscript.

An example of a CIF meeting these minimal requirements can be downloaded from here.

Additional Information Policy

Authors often decide to include more information into the cif file than the “minimal requirements”. We strongly encourage authors to include as much information as possible; the more information that you include in the CIF, the more valuable the data is to other researchers, and the higher the likelihood that your results will be used and cited by others! Please make sure that all of the data is consistent with the manuscript (distances/angles, refinement details, etc.). If structure factors are submitted, they have to be formatted using the cif syntax and to be included in the cif file to make sure they can easily be used by other authors.

An example of a CIF that includes extended information can be found here. Further details in the AmMinCifGuide.pdf

Creating A CIF

Most modern diffractometer control software packages, data reduction software, and structure refinement programs will produce a CIF for you. They will also produce data tables from the CIF. You are strongly recommended to use these facilities to avoid any manual editing of crystallographic data, and thus avoid inevitable "cut and paste" errors. The recommended sequence of tasks for producing a CIF is:

1. Perform data collection and reduction, and then structure refinement.
2. Collate the CIF fragments produced in each step to one cif for one structure.
3. Validate the CIF at the IUCr (http://journals.iucr.org/services/cif/checking/checkbasic.html)
4. If more than one structure refinement is being reported, join the individual cifs together in to a master CIF, and lock it against any editing.
5. Create the data tables and figures for the manuscript from the data in the master CIF.
6. Submit the manuscript and the CIF.

Quality Checklist

1. The cif is free of syntax errors/warnings from encifer (more info about encifer available at the link above)
2. All the data are correct and correspond to the tables in manuscript
3. The chemical composition is correct; the formula_sum matches the refined structure (site occupancies)
4. There are no significant warnings given by checkcif
5. I understand that the TETeam will laugh at me and happily reject the cif if it does not match the requirements.

CIF Resources

American Mineralogist CIF guide: AmMinCifGuide.pdf and example here:

IUCr cif resources: http://www.iucr.org/resources/cif

IUCr Cif Guide for authors: http://journals.iucr.org/b/services/cifguide.html

IUCr online cif checker: http://journals.iucr.org/services/cif/checking/checkbasic.html

Encipher program to edit cifs: http://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/EnCIFer.aspx

publCIF for checking CIFs and producing tables: http://journals.iucr.org/services/cif/publcif

Program to remove illegal characters from a CIF: www.rossangel.com

Program to tabulate data from multiple data blocks in one cif (for example from variable P or T studies) www.rossangel.com

You can download a Minimal CIF - here.

You can download a Maximal CIF - here.