Hi Sena, I would add this command helices_strands_only=True to force autobuild to just try and build helical segments. This probably won't fix the lack of connectivity however. All the best, Tom T Hi Everyone, Is there a way to force phenix (autobuild) into building a contiguous double stranded DNA. Currently, when I am solving a protein-DNA complex using SAD data: 1) its not recognizing that DNA needs to be double stranded, so it is fitting one of the strands correctly (at least part of it), but the other strand is in the protein density region. 2) It breaks down each of the strand. So it is not fitting as a contiguous 30 mer but instead a 10 mer, two 6 mers and a 8 mer. Thanks Sena