<div dir="ltr">Hi Wolfram,<div><br></div><div>It turned out that secondary structure restraints are not symmetry-aware. I'm sorry for my previous misleading response. </div><div>In example of 9dna you pointed out, one can manually set custom bonds that can go across symmetry by adding the following to parameter file:</div><div><br></div><div><div>geometry_restraints.edits {</div><div> excessive_bond_distance_limit = 10</div><div> bond {</div><div> action = *add delete change</div><div> atom_selection_1 = resid 1 and name N1</div><div> atom_selection_2 = resid 8 and name N3</div><div> symmetry_operation = y,x,-z+1</div><div> distance_ideal = 2.9</div><div> sigma = 0.1</div><div> slack = None</div><div> }</div><div>}</div></div><div><br></div><div>Also note that standard base-pair hbond restraints also include angle. There is currently no way to set angle restraints across symmetry.</div><div><br></div><div>I'll edit documentation accordingly.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Mar 24, 2017 at 8:08 PM, Oleg Sobolev <span dir="ltr"><<a href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Wolfram,<div><br></div><div>I believe that secondary structure restraints are "symmetry-aware", so just try to use them. If they don't work for you, let me know.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Fri, Mar 24, 2017 at 9:52 AM, wtempel <span dir="ltr"><<a href="mailto:wtempel@gmail.com" target="_blank">wtempel@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Hello,<div>how could one restrain DNA base pairing across a crystallographic axis? Are secondary_structure.nucleic_ac<wbr>id restraints "symmetry-aware"?<div>Thank you.</div><div>Wolfram Tempel</div></div></div>
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