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

Matthias Uthoff matthias.uthoff at uni-koeln.de
Tue Apr 27 09:01:01 PDT 2021

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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