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 ToDo: add anchor for option). 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. Running it out of Docker requires an installation of OpenStructure.
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 container in "How to run the 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 file. If the tested ModelCIF file is fully compliant with the ModelCIF format, the JSON output has
-
status"completed" - no messages in the
diagnosislist -
versionof the dictionaries the file was tested against
Format violations will be listed in diagnosis.
- basic usage
- explain output
- add version of dict validated against
- remaining options
How to run the container
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how to pull the container
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how to build the container