Hi @olibclarke. So I have tried your procedure, and got some improvements. When you do local refinement, do you have a very tight mask, or that should be rather generous ? What parameters do you think can improve things in a local refinement ? I tried going down to 3 and 2 in the angular search, but that did not make a different (got rather a bit worse). I am trying to align a few alpha helices that swing outside a larger complex. Many thanks !