Ensuring the correct syntax of a CIF file is essential for the smooth and rapid processing of crystallographic data and helps provide useful information to the scientific community.
The CCDC’s CIF deposition and validation service runs a series of syntax checks on data being uploaded to make certain the data can be read by our automated systems. It is important to note the syntax checks only establish that the data are possible to interpret, this does not make any judgement on the data quality or the chemistry of the structure(s).
Should the deposition and validation service highlight issues that require attention, it is possible to fix errors by directly editing the file contents in the browser window. The warnings should provide useful information; the file contents are also colour coded to show common CIF items including data blocks, loops and data items. By saving and rechecking the file(s), syntax errors can be easily corrected as part of the deposition process.
If it is not possible to correct the CIF file as part of the deposition process, we recommend the use of the CCDC’s enCIFer program for CIF checking and editing, available as a free download. EnCIFer includes an extended range of checks and tools for c/solutions/software/encifer/orrecting CIFs.
A comprehensive check of the consistency and integrity of crystal structure determinations in CIF format is available through our web deposition service with the integration of the IUCr’s CheckCIF service.
The IUCr’s CIF dictionary provides an up-to-date list of CIF data names, including the expected data value (e.g., number, text, permitted range etc.). Should particular data items cause syntax errors it is possible to include the text as a comment, by preceding the text with a # symbol (the CIF deposition and validation service will highlight such comments in green text).
If you are unable to upload an error-free CIF file, or have data in other formats, please email the CCDC’s deposition team on where we will endeavour to assist you.
- The enCIFer user guide contains useful information on the CIF file, and on checks and errors (chapter 6). You can read it here.
- Read also the FAQ: Are there any tools available to help produce a CIF?
- Learn more about the CIF file and signs of problems with the CIF lecture material from DECOR.
Here is a selection of FAQs from our website that could help you with your CIFs. You can read more on our FAQs page.
- Radiation probe:
- Can I deposit large CIFs that include reflection data?
- How should I name data_ values in the CIFs I am depositing?
- I do not understand what is meant by a particular error message in enCIFer, so how do I resolve the problem?
- Can I customise enCIFer to check for the presence of specific data items, required by a particular journal publisher or crystallographic database?
You can also find relevant information in the following publications:
- checkCIF validation ALERTS: what they mean and how to respond – A. L. Spek, Acta Cryst. (2020). E76, 1-11 10.1107/S2056989019016244
- Obtaining the best results: aspects of data collection, model finalization and interpretation of results in small-molecule crystal-structure determination – A. Linden, Acta Cryst. (2020). E76, 765-775 10.1107/S2056989020005368.
- Some reflections on symmetry: pitfalls of automation and some illustrative examples – W. Clegg, Acta Cryst.(2019). E75, 1812-1819 10.1107/S2056989019014907