<div dir="ltr"><div><div>Dear Zhe, <br><br></div>I think Phenix can handle it without the need of specifying whether it will be A or B. These might be too "strong" constrains in a way from my point of view. <br><br></div><div>Your DNA may be mostly B if it is unmodified, with the exception of some part of the helix that has some C3´-endo puckers and therefore there "it would be A", say. By default the nucleic acids restraints are on, I would just keep working and refining, safest way to go indeed is to place the phosphates where they should be, Phenix will take care of assigning the puckers. <br><br>If you want to compare your dsDNA with an ideal A type of helix DNA or B type of helix DNA, you can just build yourself some withing coot. You find this option under calculate/other modelling tools/ideal RNA/DNA. <br><br></div><div>I hope this helps, <br><br></div><div>Best wishes, <br><br></div><div>Almudena<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-02-23 4:50 GMT+01:00 Zhe Li <span dir="ltr"><<a href="mailto:lizhelizhelizhe@hotmail.com" target="_blank">lizhelizhelizhe@hotmail.com</a>></span>:<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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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr">Almudena Ponce-Salvatierra<div>Macromolecular crystallography and Nucleic acid chemistry</div><div>Max Planck Institute for Biophysical Chemistry</div><div>Am Fassberg 11 37077 Göttingen</div><div>Germany</div><div><br></div></div></div>
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