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<p>Dear Tynan</p>
<p><br>
</p>
<p>Because the residue numbers 121 and 1301 are not consecutive, the
refinement program does not know that they are linked. <br>
</p>
<p>But it is not possible to make the numbers consecutive, there is
the same problem with branched glycans.<br>
</p>
<p><br>
</p>
<p>In Coot, you have a Glyco module in the menu (different places
depending on the version of Coot)</p>
<p>that allows you to make the link between asparagine and
N-acetylglucosamine. This link will be written in <br>
</p>
<p>the header of the output PDB file, you will have to check it
remains in place throughout refinement. <br>
</p>
<p><br>
</p>
<p>Moreover, I make a link.edit file to restrain the link, or you
can also try to push it through ReadySet.</p>
<p>Check the output PDB for the presence of the LINK record. You
also want to avoid re-adding a hydrogen</p>
<p>atom on the linking atom (N between ASN and NAG, O between 2
sugars), because that would cause repulsion.</p>
<p><br>
</p>
<p>all the best</p>
<p><br>
</p>
<p>Julie<br>
</p>
<p><br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 08/08/22 23:38, Tynan Young wrote:<br>
</div>
<blockquote type="cite"
cite="mid:SJ0PR02MB8657B4DFD55A2C7329F5643FD4639@SJ0PR02MB8657.namprd02.prod.outlook.com">
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Hi all,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
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<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
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).</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
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.�</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
Is there some naming scheme that avoids this issue?</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
Any help is greatly appreciated. Thank you.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
Tynan</div>
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<div class="moz-signature">-- <br>
_______________
Julie Bouckaert , chercheur CNRS UMR 8576 � l�Universit� de Lille
<a class="moz-txt-link-freetext" href="http://ugsf-umr-glycobiologie.univ-lille1.fr/spip.php?article217&lang=fr">http://ugsf-umr-glycobiologie.univ-lille1.fr/spip.php?article217&lang=fr</a>
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