you can combine the two merged datasets with CAD and scale them together with 
Scaleit: see ccp4i -> Experimental phasing -> Data preparation -> Combine 
datasets with CAD, Scale and Analyse datasets

Or you could give the unmerged files different dataset names, combine them in 
Pointless and scale them together in Scala, but that's probably not necessary

Phil

On 12 Jul 2010, at 21:53, Subhangi Ghosh wrote:

> Hi All,
> 
> I have two different datasets of the same protein, for example dataset A and 
> dataset B. I want to make a difference map of [ Fo (of set A) - Fo (of set 
> B)]. (I'll use phases of another solved structure from an isomorphous 
> crystal). For this I'll have to scale two different mtz files (associated 
> with set A and B respectively) but keep them separate after scaling. Is there 
> anyway that I can do this?
> 
> Thank you,
> Subhangi

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