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 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 ------------------------------------------------------------------------ ------------------------------------------------------------ -SECURITY/CONFIDENTIALITY WARNING-

This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) ------------------------------------------------------------

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] -- _______________ Julie Bouckaert , chercheur CNRS UMR 8576 à l’Université de Lille http://ugsf-umr-glycobiologie.univ-lille1.fr/spip.php?article217&lang=fr Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) IRI, Office 131, 50 Avenue de Halley, 59658 Villeneuve d’Ascq, France Tél. +33 (0) 362 53 17 29 Mobile +32 (0) 498 57 14 65