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

Pavel Afonine pafonine at lbl.gov
Mon Mar 4 17:53:29 PST 2019

Hi Julian,

perhaps you can approach this by defining custom bonds between symmetry 
copies, like this:

refinement.geometry_restraints.edits {
   bond {
     atom_selection_1 = chain A and resseq 123 and name N
     atom_selection_2 = chain B and resseq 321 and name OD1
     symmetry_operation = -x-1/2,y-1/2,-z+1/2
     distance_ideal = 2.1
     sigma = 0.02


On 3/1/19 17:22, Julian Esselborn wrote:
> 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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