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Hi Jiang Xu,<br>
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(Phenixbb added as I suspect this is Phenix not coot that has caused your issue)<br>
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Did you check the "add hydrogens" button in Phenix.refine? Sometimes this can erroneously add a second H to the ND of glycosylated Asn residues. (I assume this is because bond distances in the input PDB file fall outside Phenix's definitions of an Asn-NAG link).</div>
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If the second H is added, this breaks the refinement of the Asn-NAG bond.<br>
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My work around is to run "Ready Set" to add hydrogens as a separate job, and then manually inspect and correct the Asn residues as necessary before running Phenix.refine and _not_ checking the "add hydrogens" box.</div>
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I hope this fixes your problem.</div>
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Good luck,</div>
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Dave</div>
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--<br>
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Dr David C. Briggs<br>
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Senior Laboratory Research Scientist<br>
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Signalling and Structural Biology Lab<br>
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The Francis Crick Institute<br>
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London, UK<br>
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==<br>
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about.me/david_briggs</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jiang Xu <foxjuly@GMAIL.COM><br>
<b>Sent:</b> Tuesday, June 22, 2021 6:47:36 AM<br>
<b>To:</b> CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK><br>
<b>Subject:</b> [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine</font>
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Use caution.</span></div>
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<div dir="ltr">Hello guys,
<div> I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain
to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a dashed line, rather than a solid line in Coot. After refinement of the structure using Phenix.refine,
I found the bond just disappeared, and the amine group still has two hydrogen atoms, which should contain one hydrogen atom. So, how to solve this problem? </div>
<img src="cid:ii_kq7mfk030" alt="image.png" width="267" height="245" style="margin-right:0px"><br>
<div>Thank you,</div>
<div>Best,</div>
<div>Jiang Xu</div>
<div>Lin Chen's Research Group</div>
<div>University of Southern California</div>
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