To the point of refining in Phenix, once you have the glycans in place it
should be automatic except for the first link of the tree. Send me the
model and I can provide the necessary files for refinement.
Cheers
Nigel
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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bi
In the monomer library, pyr-SER and pyr-THR links are defined for the
O-glycosylation. A monomer should belong to the "pyranose" group in
the library (or in a user-provided dictionary).
Best regards,
Keitaro
On Fri, 14 Jul 2023 at 09:22, Jon Agirre
<17a7df66b7b3-dmarc-requ...@jiscmail.ac.uk>
On 14/07/2023 08:52, Jonas Emsley wrote:
Dear All
We have a crystal structure with O-glycans for the first time attached
to a Ser and a Thr sidechain
If anyone can recommend the procedure for adding these in coot and
refining them in phenix /refmac that would be greatly appreciated
Hi J
To the best of my knowledge, there is no o-glycan equivalent of the Coot
glyco plugin. We (as in YSBL, York) are working with others to provide
tools to build all kinds of glycans, but there's nothing you can use at
this point.
I would deal with it like I'd do with other modifications, get monomer,
Dear All
We have a crystal structure with O-glycans for the first time attached to a Ser
and a Thr sidechain
If anyone can recommend the procedure for adding these in coot and refining
them in phenix /refmac that would be greatly appreciated
All the best
jonas
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