Dear Tynan
Because the residue numbers 121 and 1301 are not consecutive, the
refinement program does not know that they are linked.
But it is not possible to make the numbers consecutive, there is
the same problem with branched glycans.
In Coot, you have a Glyco module in the menu (different places depending on the version of Coot)
that allows you to make the link between asparagine and
N-acetylglucosamine. This link will be written in
the header of the output PDB file, you will have to check it
remains in place throughout refinement.
Moreover, I make a link.edit file to restrain the link, or you can also try to push it through ReadySet.
Check the output PDB for the presence of the LINK record. You also want to avoid re-adding a hydrogen
atom on the linking atom (N between ASN and NAG, O between 2 sugars), because that would cause repulsion.
all the best
Julie
Hi all,
I am having issues with naming of glyco- groups and refining my glycosylated EM structure in Coot. I have noticed that many models use the same chain ID for the glyco- groups as the chain ID they are attached to (i.e. NAG/B/1301 would be linked to ASN/B/121).
When working with the model in Coot, I would like to refine only the ASN 121 and the NAG 1301 attached to it. However, due to the naming of the glyco- group, Coot will refine residues 121-1301. Not only is this very time-consuming, but it will disrupt the rest of the model - which I do not want to do. If I change the chain ID of the glyco- group to an altogether different chain ID, then I can no longer refine both the side chain and the glyco- group.�
Is there some naming scheme that avoids this issue?
Any help is greatly appreciated. Thank you.
Tynan
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