[phenixbb] Refinement of a b-Strand swapped into the sheet of the symmetry related copy
osobolev at lbl.gov
Wed Apr 28 11:02:56 PDT 2021
You may try to specify H-bonds manually using custom bond restraints
mechanism which supports bonds over symmetry:
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.
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 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
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