Currently the most recent release of Biopython (1.6.8) doesn't parse mmtf files correctly (altlocs and disordered flags are set wrong). The developmental release does, however for now if a user has 1.6.8, cleaning structure files doesn't work properly when mmtf is set as the default. So for now -- mmcif will be set as the default file format until the next Biopython release.
Currently the most recent release of Biopython (1.6.8) doesn't parse mmtf files correctly (altlocs and disordered flags are set wrong). The developmental release does, however for now if a user has 1.6.8, cleaning structure files doesn't work properly when mmtf is set as the default. So for now -- mmcif will be set as the default file format until the next Biopython release.
See biopython/biopython#975