The default unit cell and symmetry for the "fitted" model (the one that was moved) is the unit cell and symmetry of the "fixed" pdb. As I am superimposing the same model from several space groups to study the differences in packing, I need the "fitted" pdb to keep its own unit cell and symmetry. How might I do this?
Could you run the superposition "the other way around", i.e. instead of fitting A to B fit B to A.
When is the current default of altering the unit cell and symmetry of the moving model useful?
In general, you cannot arbitrarily move a model with respect to the crystallographic symmetry; you will get clashes due to symmetry. If you fit B so that it is in the same place as A, and assuming A has no clashes due to symmetry, then B should have no clashes, too. Ralf