[phenixbb] Naming/refining glycosylation

[David Briggs]

Hi Tynan,

I'm assuming you are using coot 0.9.x

To refine N-linked glycans (also disulfides) you can:

1) use "sphere real-space refine" (default hot key Shift-R) whilst centred on the Asn side chain

2) use "refine tree" in the glyco module.

Hth,

Dave



Dr David C. Briggs CSci MRSB

Principal Laboratory Research Scientist

Signalling and Structural Biology Lab

The Francis Crick Institute

London, UK

==

about.me/david_briggs<http://about.me/david_briggs>

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From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Tynan Young <tyoung at coh.org>
Sent: Monday, 8 August 2022, 22:41
To: phenixbb at phenix-online.org <phenixbb at phenix-online.org>
Subject: [phenixbb] Naming/refining glycosylation


External Sender: Use caution.

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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