[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 

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 

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 Esselborn
Postdoctoral Researcher
Tezcan group
University of California, San Diego

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