<div dir="ltr">Hi Brandon,<br><div><br></div><div>There is a small hint here: </div><div><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><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">For bonds to symmetry copies, specify the symmetry operation in xyz notation, for example:<br>symmetry_operation = -x-1/2,y-1/2,-z+1/2</blockquote><div><br></div><div>The whole .eff file might look like:</div> refinement.geometry_restraints.edits {<br> bond {<br> action = *add delete change<br> atom_selection_1 = chain A and resid 1199 and name O4<br> atom_selection_2 = chain A and resid 1196 and name C1<br> symmetry_operation = X-1/2,-Y+1/2,-Z<br> distance_ideal = 1.439<br> sigma = 0.020<br><div> }</div><div>} </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 Fri, May 22, 2020 at 3:55 PM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</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">
<div>
Hi Brandon,<br>
<br>
<blockquote type="cite">
I
have an unusual problem in which my enzyme (a dimer) is covalently
bound to its own C-terminus and so is daisy-chained across the
crystal lattice. In the past, I have encountered and fixed this
problem by extracting the covalent part of the molecule and
re-phasing using that as the molecular replacement model. In this
case, I am not able to due so. When I input the restraints, it
either crashes refine or attempts to impose them on the
corresponding residues within the ASU (understandable) but they
are quite distal and this leads to "interesting" refinement
results. Is there a good way of making phenix.refine do what I
want? Or perhaps a workaround that I haven't considered yet?<br>
</blockquote>
<br>
this should be possible but I don't remember what it takes. If you
send me the file I might be able to figure this out.<br>
<br>
Pavel<br>
</div>
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