There might be many reasons..
Do you have a spacegroup with alternate indexing? If so the two crystals
may not be using the same convention.
See $CHTML/reindexing.html for more details.
Or is one data set a high resolution pass and one a low resolution pass?
Sometimes then there are
Dear CCP4,
I have a couple of datasets native and heavy-atom-derivatized. The spacegroup
and cell dimensions of all are the same (or very similar). For some reason
I cannot merge any of the datasets together. If for example I rescale one
native dataset by itself, my Rmerge is about 10%,
