# [phenixbb] Distance constraint to atom in symmetry copy in phenix.refine

Julian Esselborn julian.esselborn at rub.de
Fri Mar 1 17:22:12 PST 2019

Dear community,
we have a somewhat complicated problem to which I don't seem to find a
solution.

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.
However, we have three cases of these axes:
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.
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.
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.

Cases (2) and (3) are pseudo-symmetric in the crystallographic sense.

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.

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.
Is there a way to set a distance constraint such that it measures the
distance to a crystallographic symmetry copy?

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).

I'm a bit at a loss how to deal with this and would appreciate input.

Thanks a lot in advance!

all the best

Julian

----
Julian Esselborn
Postdoctoral Researcher
Tezcan group
University of California, San Diego

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