checkCIF/PLATON report

checkCIF Frequently-Asked Questions (FAQ)

• What is checkCIF?

checkCIF on the Web

• How do I use checkCIF?
• What options are available?
• Can I use checkCIF to submit a paper?

Data Validation checks

• What is Data Validation?
• What does Alert Level A signify?
• What does Alert Level B signify?
• What does Alert Level C signify?
• What is a Validation Response Form?

What is checkCIF?

checkCIF is the IUCr service for checking submissions in CIF format to its own and and other journals. Prospective authors may submit their CIF manuscripts by email or via a web interface, and receive a check report by return email or as a web page.

checkCIF on the web

How do I use checkCIF?

Web interface
checkCIF is at

• checkCIF for full publication checks
• checkCIF for basic structural checks.

Enter the full path name of a CIF on your local computer system in the text entry box, or use the Browse... button to locate the desired file. Send the file for processing by clicking on the Send CIF for checking button. Processing and return of the results may take several minutes, depending on file sizes, available network bandwidth and load on the server computer.

What options are available?

• Basic structural check. This basic structural check contains a subset of the full checkCIF/PLATON tests and includes checks on: 
  • CIF syntax and construction
  • Cell and geometry details
  • Space-group symmetry


• Full publication check. This applies the complete set of integrity and data validation tests for a submission to an IUCr journal and includes checks on:
  • CIF syntax and construction
  • Cell and geometry details
  • Space-group symmetry
  • Anisotropic displacement parameters
  • Publication items
  • Structure factors

Can I use checkCIF to submit a paper?

Not at present. There are plans to develop the web interface to allow this in due course.

For the moment, an intending author must use checkCIF prior to submission. If the web version of the program indicates that there are possible problems, an author should

• copy the Validation Response Form (VRF) from the browser report window to the local filesystem
• complete the form with information explaining or justifying the suspect results
• add the completed form to the CIF before submission

Data Validation checks

What is Data Validation?

Data validation is the process of checking structural submissions to IUCr journals for internal consistency and ability to meet the standards required for publication. Three levels of test are applied:

• The prefilter checks that a complete set of information is present, as required by the Notes for Authors.
• CIF consistency checks test the consistency of mutually dependent CIF data items, according to a set of published criteria.
• Geometry and symmetry checks assess the reasonableness of the reported structure using the PLATON software package.

Results are returned in the form of a listing of anomalies, ranked by severity. In the web form of checkCIF, there is a hyperlink from each error message to a description of the algorithm or criteria applied. This explanation appears in the information pane of frames-capable browsers.

What does Alert Level A signify?

Possible problems detected by the data validation software are assigned different levels of severity. Alert level A indicates that a potentially serious problem with the data has been detected.

What does Alert Level B signify?

Possible problems detected by the data validation software are assigned different levels of severity. Alert level B indicates that a potential problem with the data has been detected. Its occurrence usually indicates, individually or with other alerts, that some corrective action is required.

What does Alert Level C signify?

Possible problems detected by the data validation software are assigned different levels of severity. Alert level C indicates that an outlier to the defined standards has been detected and that this may need to be corrected. When correlated with alerts from other tests, it may signal more serious problems.

What is a Validation Response Form?

The Validation Response Form (VRF) is a portion of text in CIF format supplied in the checkCIF report that

• indicates the problems that have triggered Alerts at level A or B
• provides a field for the author to respond to the alert

If you intend to submit a CIF for publication in an IUCr journal, you should attempt to resolve the more serious problems (level A or B) before submission. This may involve additional measurements or structure refinements. However, the nature of your study may justify the reported deviations from the submission requirements of the journal. If this is the case, you can insert an explanation in your CIF using the Validation Reply Form (VRF). Your explanation will be assessed as part of the review process.

It is preferable for explanatory text to be placed in the relevant fields in the CIF such as _publ_section_exptl_refinement. If the explanation of a problem is given in the CIF in this way, the corresponding entry in the VRF may simply read `see _publ_section_exptl_refinement'.

Here is an example of a completed VRF:

_vrf_PLAT_213_global
;
PROBLEM:  Atom C(6B)  has ADP max/min ratio ............      5.20           
RESPONSE: 
           Atom C6 of the ring (B) was found to be disordered; see
           _publ_section_exptl_refinement
;

The completed VRF should be inserted in the CIF after the first datablock identifier (i.e. after the data_something line that indicates the start of a CIF data block).

Ideally, the VRF should be added to the CIF using publCIF.