The difference is that the mmCIF reader was split off from the CIF reader.
In the past, the CIF reader included all the macromolecule code, and
somewhere along the way of reading it all Jmol determined that it was mmCIF
and not CIF. That is a difference recently introduced. Actually it doesn't
matter if a normal CIF file is read as mmCIF -- it just isn't efficient in
reading code; but as you see, if there is no marker now for mmCIF, the
structure will be read fine as CIF and then not be able to use its
secondary structure, biomolecules, etc.
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