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As far as I understand you avoid such pitfalls and pain if you use XDS:
a) it gives you a clear warning when several indexing possibilities exist,
and it is a piece of cake to reindex your data with any of the given
(sic!) matrices.
b) you can give a reference data set so that you do not mis-index your
data .
Tim
And of course d*TREK does the same.
But unless I know in advance which way (eg) CNS will index its Fcalc data
set, there is still a 50% chance that I will choose the other option, as
neither is right nor wrong, in an absolute sense, but only right or wrong
with respect to (eg) CNS's arbitrary choice.