Do it the same way we used to do all glycans last year, before the new
Coot interface for adding glycans:
* "Get monomer" to get the monomer you want to add roughly where it goes.
* Remove hydrogens from it.
* Position the O1 atom roughly where you have the O-gamma of Ser/Thr,
rotate and translate to move the sugar into density.
* Make sure you have the right anomer (chirality at C1 carbon), so you
end up with beta-n-acetylglucosamine, or whatever fancy brand of glycan
you have.
* Remove the O1 atom from the sugar monomer.
* Merge the new monomer into your molecule, renumber and/or change chain
ID as you like it (PDB will change it again probably).
* Save coordinates and go to your favorite reciprocal-space refinement
program. phenix.refine and refmac know some of the O-linked glycan
linkages, and will be able to figure out those restraints automatically.
Depends on your glycan.
(The instructions above are from memory, and are not tested.)
Engin
On 7/23/18 5:07 PM, Goran Bajic wrote:
Hi all,
I may have an O-linked glycan in one of my structures and I was
wondering if someone has any experience building these? I think COOT
only handles N-linked glycans.
Thanks,
Goran
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