Mapman (Uppsala software factory) allows you to subtract maps if they are on the same grid. You may need to multiply one map by a factor (again in mapman) to make the background flat in the regions you believe to be identical.
Linearity of the Fourier Transform implies you could get the same result by subtracting in reciprocal space. However if the crystals are not perfectly isomorphous, it may help to "skew" one map onto the others before subtracting, i.e. apply a rotation-translation operator to superimpose equivalent areas, which could be a reason for doing it in real space. You can do this with "mave" (also USF), getting the operator by superimposing models in O or lsqman, or, if the refinement has not progressed that far, refining the operator from identity with the "improve" option of mave. I expect mapmask and friends of dmmulti can do all this too, but I am less familiar with the CCP4 tools. Either way, there is certain amount of documentation you will need to read in order to "know how to use it". But that is time well spent in the long run, as it will help you to interpret the results or modify the procedure as new situations arise. If you get stuck and have specific questions, the BB is hear to help! Ed
