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Hi Julian,<br>
<br>
perhaps you can approach this by defining custom bonds between
symmetry copies, like this:<br>
<br>
<tt><font size="-1">refinement.geometry_restraints.edits {<br>
bond {<br>
atom_selection_1 = chain A and resseq 123 and name N<br>
atom_selection_2 = chain B and resseq 321 and name OD1<br>
symmetry_operation = -x-1/2,y-1/2,-z+1/2<br>
distance_ideal = 2.1<br>
sigma = 0.02<br>
}<br>
}<br>
</font></tt><br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/1/19 17:22, Julian Esselborn
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:72fc0b95-cedf-db43-ba2e-5d380cf5de0c@rub.de">Dear
community,
<br>
we have a somewhat complicated problem to which I don't seem to
find a solution.
<br>
<br>
We have a structure, which has a number of 3-fold and 2-fold
symmetry axes in the final assembly structure. The 3-fold axes are
hold together by metal atoms on the axis.
<br>
However, we have three cases of these axes:
<br>
1. Symmetry axis falls onto the crystallographic symmetry axis. We
can deal with this; setting metal to 0.33 occupancy and setting
metal-protein distance constraints. This is a proper symmetry
axis.
<br>
2. Symmetry axis doesn't fall onto a crystallographic symmetry
axis, but all three monomers coming together are within the same
symmetry copy of the ASU. Even easier, metal stays at occ=1 and we
just set constraints to chain A, chain B, chain C.
<br>
3. The really challenging case, where the axis doesn't fall onto
the symmetry axis, but the three monomers coming together are in
different symmetry copies of the ASU.
<br>
<br>
Cases (2) and (3) are pseudo-symmetric in the crystallographic
sense.
<br>
<br>
Usually a bit of intelligent moving around of the monomers to
their crystallographic symmetry positions should push all monomers
of case (3) into neighboring positions within the same ASU ending
up as case (2); problem solved.
<br>
<br>
BUT: In our structure we have too many 3fold axes, such that there
will always be one of them ending up as case (3). E.g. the three
monomers are chains A, B, C, but they do not end up neighboring in
the ASU. Rather the axis is formed by A, B' and C'' (with '
denoting different symmetry copies of the ASU). We could assign
the metal to chain A with occ=1 and no metal in B and C. However,
we would need to set a distance constraint from the metal to it's
ligands in protein monomer B and protein monomer C. But it is only
the ligand in B' and C'', which are actually close to the metal in
A. The ligands in B and C are at the other end of the ASU.
<br>
Is there a way to set a distance constraint such that it measures
the distance to a crystallographic symmetry copy?
<br>
<br>
A different idea was to just assign an alternative position alt A,
alt B and alt C to the metal, with A being close to the ligand in
monomer A, B close to monomer B and C close to monomer C. That way
we could make constraints. But we would need to cross fingers that
the three metal atoms actually end up in the same spot once
applying the crystallographic symmetry (and remember, that 3-fold
axis is not constructed by applying a 3fold rotational symmetry
around that axis; rather an actual crystallographic symmetry
somwhere else brings them together; means the ligands with their
metal atoms can actually move independently).
<br>
<br>
I'm a bit at a loss how to deal with this and would appreciate
input.
<br>
<br>
Thanks a lot in advance!
<br>
<br>
all the best
<br>
<br>
<br>
Julian
<br>
<br>
<br>
<br>
----
<br>
Julian Esselborn
<br>
Postdoctoral Researcher
<br>
Tezcan group
<br>
University of California, San Diego
<br>
</blockquote>
<br>
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