[phenixbb] Refinement of a b-Strand swapped into the sheet of the symmetry related copy

[Oleg Sobolev]

Hi Matthias,

You may try to specify H-bonds manually using custom bond restraints
mechanism which supports bonds over symmetry:
https://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles
You will not get angle restraints around H-bonds in this case.

I believe the most straight-forward approach would be to take Bruno's
suggestion about expanding the molecule and apply NCS constraints to ensure
the copies stay identical.

Best regards,
Oleg Sobolev.

On Tue, Apr 27, 2021 at 9:04 AM Matthias Uthoff <
matthias.uthoff at uni-koeln.de> wrote:

> Hi phenixbb,
>
> I am working on a homodimer. Each protein has an internal b-sheet with
> three b-strands, however the sheets swap their middle strands. So a
> sheet consists of one strand from molecule A surrounded by two strands
> from molecule B or vice versa. As I am at 3 A resolution, I would like
> to set secondary structure restraints including correct hydrogen bonding
> between the strands of the two molecules.
>
> My problem: There is only one protein in the ASU and the "other"
> molecule is in deed just a symmetry mate.
>
> Phenix is not able to automatically detect this and if I provide the
> restraints myself, phenix discards them as it is falsely assuming the
> b-sheet is intramolecularly (all on chain A) and hence the strands are
> 30ish A apart.
>
> What is the best way of refining this feature?
>
> Thanks in advance,
>
> Matthias
>
> --
> Matthias Uthoff, PhD Student
>
> University of Cologne
> Institute for Biochemistry
> Zülpicher Straße 47
> D-50674 Cologne
>
> Phone: +49 221 470 3211
> E-Mail:matthias.uthoff at uni-koeln.de
> Internet:http://px.uni-koeln.de
>
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