Symmetry refinement


I am trying to refine a structure, which has true D1 symmetry and C7 Pseudo symmetry.
C1 refinement worked out well and gave me 3A map with small but nice asymmetric features.
However, when I impose D1 symmetry, I got D7 like structure with averaged out features.

I am aware that this kind of averaging issue can always happen when we work with pseudo symmetry molecules. One thing confuse me why C1 worked, while D1 didn’t. orientation search with D1 should allow more accurate orientation than C1 as particles just got refined along cross common line.

Got very curious how the orientation search and reconstruction goes with symmetry impose.
Any possible explanation or comment will be greatly appreciated.


Most likely the symmetry axis was not aligned according to the convention; it’s also highly unusual to use D1 as opposed to C2. I would recommend that you align your symmetry axis to the z-axis of the box and apply C2.