[phenixbb] Naming/refining glycosylation

julie julie.bouckaert at univ-lille.fr
Mon Aug 8 21:54:42 PDT 2022

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


On 08/08/22 23:38, Tynan Young wrote:
> 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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_______________ Julie Bouckaert , chercheur CNRS UMR 8576 à l’Université 
de Lille 
Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) IRI, Office 
131, 50 Avenue de Halley, 59658 Villeneuve d’Ascq, France Tél. +33 (0) 
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