I had a very similar problem with data collected on a particular beamline.  The 
issue was that I had to reverse the spindle direction in imosflm settings.  
Also, when I load data from this beamline into imosflm the program rotates the 
images by 90 degrees for some reason (this does not happen in HKL2000).  
Because of this rotation, the beam center that I used in HKL2000 was different 
than the beam center position for imosflm.

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