I tried supplying the space group in the command line using the --symmetry I think there is another bug there - the command line symmetry does not override the (wrong) symmetry that the routine gets from the .sca file

I am afraid you are right again. I forgot to include the plumbing for the --force_symmetry option. Sorry, this is getting ugly. To use your unmerged reflection file, edit this Python script in the iotbx tree: echo `libtbx.show_dist_paths iotbx`/iotbx/scalepack/no_merge_original_index.py Replace all "force_symmetry=False" with "force_symmetry=True", then try again.