On 17/04/2024 21:07, Markus Meier wrote:
Hi Paul,
thank you for implementing the Glyco module in Coot!
It is not in Coot 1 (yet). It needs to be rewritten.
I used its "Add N-linked Glycan" function to build an N-linked glycan
which contains L-fucose with an alpha1-6 glycosidic linkage on the
first N-acetyl glucosamine of the tree.
However, after exporting the tree, I checked it with privateer and
unfortunately privateer flags the L-fucose as having the wrong
anomeric linkage - beta 1-6 :-(
Coot reports the same as being in the alpha 1-6 anomeric form.
How was the apparent? Did you use print_glyco_tree()?
I then manually built the opposite anomeric form which privateer
happily accepts as being alpha1-6. However, Coot reports it as beta 1-6.
In my understanding, the alpha configuration of a glycosidic linkage
should have the oxygen at the anomeric centre and the -CH3 group at
opposite faces of the sugar ring, so I have to agree with privateer on
this one.
Please check you code.
OK, will do.
I have attached the two glycan trees and here is the output of
privateer and Coot for both. Coot and privateer versions are given at
the bottom.
Btw. Neither privateer nor refmac5 can read the mmCIF files that Coot
produces with the "Extract this Tree" functions. All the
_atom_site.label_*_id entries are empty!
Oof. Cif.
OK. I'll take a look after the release.
Paul.
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