ModelCIF validation tool
This is a tool to check that the formatting of ModelCIF files complies with the ModelCIF format declaration (aka "dictionary"). Upon successful validation, a ModelCIF file can be extended with the dictionary version the file was compared to (option --extend-validated-file). For more basic mmCIF validation, the dictionary of the underlying PDBx/mmCIF format is also available.
The easiest way to run validation is from Docker container.
The tool itself is a wrapper around the CifCheck tool by RCSB.
If you have questions about ModelCIF validation, feel free to contact the MA team.
- ModelCIF validation tool
- Files in this directory
How to run the validation tool
This is just a description of the validation tool itself. When running it from inside a container, the command needs to be prefixed with the instructions to start the container. Find information for running the validation Docker container in "How to run the Docker container".
Upon completion, if there hasn't been any error running the command, the validation tool returns a concise report in JSON format. That output is meant to be input to a website or any kind of nicely formatted report. Output can also be stored as a JSON formatted file. If the tested ModelCIF file is fully compliant with the ModelCIF format, the JSON output has
-
status"completed" - no messages in the
cifcheck-errorslist - no messages in the
diagnosislist -
versionsof the dictionaries the file was tested against
Format violations will be listed in diagnosis.
cifcheck-errors gathers errors from the CifCheck command. This has nothing to do with wrong formatting - messages in this list mean that CifCheck has "crashed". This should not happen, possible issues with CifCheck should be caught by the validation tool. Feel free to report them to the MA team.
The most basic way to invoke the validation tool is just with a ModelCIF file (example shows the command plus possible output):
$ validate-mmcif-file model.cif
{"cifcheck-errors":[],"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.361","location":"https://raw.github.com/ihmwg/ModelCIF/master/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.3","location":"https://raw.github.com/ihmwg/ModelCIF/master/archive/mmcif_ma-v1.4.3.dic"}]}
$ Add dictionary information used for validation to ModelCIF file
Since both dictionaries, ModelCIF and PDBx/mmCIF, represent actively developed file formats, different versions exist. While extending them, quite some thinking goes into making only non-breaking changes. The idea is that a ModelCIF file formatted following dictionary version 1.3, is still valid with dictionary version 1.4. But the version number also tells you which features to expect in a ModelCIF file, so it seems like a good idea to keep the version inside the file.
The validation tool can add the version upon positive validation, enabled by --extend-validated-file (-e).
-e can take an alternative file name to write the validated ModelCIF file to, e.g. if one wants to keep the original ModelCIF file unaltered:
$ validate-mmcif-file -e validated_model.cif model.cif
{"cifcheck-errors":[],"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.361","location":"https://raw.github.com/ihmwg/ModelCIF/master/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.3","location":"https://raw.github.com/ihmwg/ModelCIF/master/archive/mmcif_ma-v1.4.3.dic"}]}
$ The last command will generate a new file validated_model.cf upon positive validation (diagnosis points to an empty list), with the versions added to the _audit_conform list inside the file.