<div dir="ltr">Dear Zhe,<div><br></div><div>Presently, there is no option to enforce the particular sugar pucker in DNA. Nevertheless, Phenix still applies restraints to sugar rings so they would stay in a particular conformation based on input geometry. So the way to go is make desired conformation for your sugars in e.g. Coot and Phenix should keep them in it. If it is not the case for you, we will need more information to investigate further.</div><div><br></div><div>Regarding to secondary structure restraints for nucleic acids, presently they enforce planarity of base-pairs, correct hydrogen bonds in base pair and parallelity of stacked bases.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Feb 22, 2016 at 7:50 PM, Zhe Li <span dir="ltr"><<a href="mailto:lizhelizhelizhe@hotmail.com" target="_blank">lizhelizhelizhe@hotmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I am refining a protein-dsDNA complex structures at 2.4-3 A. Based on the phosphate distance, I can predict if particular nucleotide is A DNA (C3’-endo) or B DNA (C2’-endo). I want to add restrain to to the specific nucleotides as A or B DNA. But secondary_structure_restraints for nucleic acid does not seem to have options for this. Any suggestions?<br>
Thanks<br>
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