What is mmCIF ?
mmCIF stands for 'macro-molecular Crystallographic Information File'. This format was developed by the PDB consortium and the International Union of Crystallography (IUCr), based on Crystallographic Information File (CIF), a format used for describing the structures of small molecules.
mmCIF became the recommended format for the exchange of biomacromolecular structures in 2014.

mmCIF and Jalview
Since Jalview 2.10, mmCIF is used for structures downloaded from the PDB. This means:

1. Jalview can use the mmCIF to read structures that are too large to be represented by a single PDB file. (ie, with more than >62 chains and/or 99999 ATOM records).
2. Jalview users will have access to the richer annotation provided by PDBx/mmCIF files.
3. There may be slight differences between sequences containing modified residues for structures downloaded in mmCIF format. This is because mmCIF differs from the PDB format in the way it describes non-standard sequence data.

Support for importing 3D structure data from flat file and EMBL-PDBe as mmCIF was added in Jalview 2.10