QS contains (hard-coded) the primitive symmetry operators corresponding to all 230
space groups as given in the International Tables. For those space groups for
which the Tables give more than one (alternative) settings, only one is supported by
the program. I have tried to stick to the most common ones (eg C2 instead
of B2, hexagonal instead of rhombohedral axes, etc), but
this doesn't mean that you should re-index your data
ignoring the good reasons that made you chose a different setting.
Instead, you can keep your favorite setting and define the corresponding symmetry operators
explicitly using the SYMMetry keyword as described on page
(do not forget to
remove the GROUP keyword from your new input file). Note that you can safely
ignore all operators arising from the presence of a non-primitive lattice.
Please also note that QS will not
make any tests on the input matrices (not even a determinant calculation), so you have
to type them carefully.