checkCIF Frequently-Asked Questions (FAQ)
checkCIF on the Web
Data Validation checks
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
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:
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.