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

Julian Esselborn julian.esselborn at rub.de
Fri Mar 22 15:58:42 PDT 2019

Thanks a lot Pavel! This was exactly what I was looking for and now I 
realized I should have seen that myself.

Worked for one of my problems, where I just needed a distance restraint. 
Unfortunately I also had one, where I would have needed a planarity 
restraint and there is no symmetry option for those I think. So I ended 
up using the alternative position workaround for that one.

Am 04.03.2019 um 17:53 schrieb Pavel Afonine:
> 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
>    }
> }
> Pavel
> 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

Dr. Julian Esselborn
AG Photobiotechnologie
Ruhr-Universität Bochum
ND 2/170
Universitätsstr. 150
44801 Bochum

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