[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
0032-27049
Universitätsstr. 150
44801 Bochum
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