>>Scenario 1)
Suppose the true cell parameters do vary and the reported esds from
integration reflect this. How would you use this information in subsequent
refinement against the merged intensity data?
If the crystal is properly bathed in the beam and not being hugely damaged, i.e., the data are being measured correctly, this is highly unlikely. But considering how often data are measured non-ideally, I see your point.
>>Scenario 2)
Suppose the true cell parameters do not vary but for some reason they
were incorrectly refined during indexing and not adjusted during data
integration. I think this is more likely for mosflm than for HKL given
the default behaviour of the two programs. In this case it is possible
that you could detect and correct the error during model refinement,
but that seems less promising than going back to the integration
program and doing additional post-refinement before merging the data.
I would think that once the structure is solved, the model itself would be a much finer measuring stick than the beamline apparatus, but I would be happy to be proven wrong. For locating/measuring the spots better, I agree with what you are saying, but for getting the cell parameters right, I can't see how it would help to go back to integration.
JPK
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