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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 saturated spots which mess up the scaling..

I usually merge both sets independently first - cad them together and 
run SCALEIT to check the degree of agreement.

SCALEIT gives a useful list of outliers and you might be able to 
pinpoint the problem from that.


Kianoush Sadre-Bazzaz wrote:
> 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%, but when I add 50 images (or so) of another, 
> supposedly isomorphous crystal, my Rmerge goes up to 20%.
>
> I was wondering if anyone has encountered a similar problem or can 
> offer any suggestions. Thanks so much,
> Kianoush
>
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