<div dir="ltr">Hi Matthias,<div><br></div><div>You may try to specify H-bonds manually using custom bond restraints mechanism which supports bonds over symmetry: <a href="https://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles">https://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles</a></div><div>You will not get angle restraints around H-bonds in this case. </div><div><br></div><div>I believe the most straight-forward approach would be to take Bruno's suggestion about expanding the molecule and apply NCS constraints to ensure the copies stay identical.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Apr 27, 2021 at 9:04 AM Matthias Uthoff <<a href="mailto:matthias.uthoff@uni-koeln.de">matthias.uthoff@uni-koeln.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi phenixbb,<br>
<br>
I am working on a homodimer. Each protein has an internal b-sheet with <br>
three b-strands, however the sheets swap their middle strands. So a <br>
sheet consists of one strand from molecule A surrounded by two strands <br>
from molecule B or vice versa. As I am at 3 A resolution, I would like <br>
to set secondary structure restraints including correct hydrogen bonding <br>
between the strands of the two molecules.<br>
<br>
My problem: There is only one protein in the ASU and the "other" <br>
molecule is in deed just a symmetry mate.<br>
<br>
Phenix is not able to automatically detect this and if I provide the <br>
restraints myself, phenix discards them as it is falsely assuming the <br>
b-sheet is intramolecularly (all on chain A) and hence the strands are <br>
30ish A apart.<br>
<br>
What is the best way of refining this feature?<br>
<br>
Thanks in advance,<br>
<br>
Matthias<br>
<br>
-- <br>
Matthias Uthoff, PhD Student<br>
<br>
University of Cologne<br>
Institute for Biochemistry<br>
Zülpicher Straße 47<br>
D-50674 Cologne<br>
<br>
Phone: +49 221 470 3211<br>
<a href="mailto:E-Mail%3Amatthias.uthoff@uni-koeln.de" target="_blank">E-Mail:matthias.uthoff@uni-koeln.de</a><br>
Internet:<a href="http://px.uni-koeln.de" rel="noreferrer" target="_blank">http://px.uni-koeln.de</a><br>
<br>
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