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

Pavel Afonine pafonine at lbl.gov
Fri Mar 22 19:38:48 PDT 2019

```Hi Julian,

questions or need any assistance! You are correct, there is no plane
restraints that are symmetry aware -- this must very tricky to implement!

All the best,
Pavel

On 3/22/19 15:58, Julian Esselborn wrote:
> 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
>>
>

```