[phenixbb] Automatic linking of glycans doesn't work when hydrogens are added by ReadySet

Luca Jovine Luca.Jovine at ki.se
Mon Apr 27 01:58:28 PDT 2015

Yes, I also saw this… a solution is to manually edit the PDB file output by phenix.read_set to get rid of HD22 of N-linked Asn residues - then phenix.refine works.



Luca Jovine, Ph.D.
Professor of Structural Biology & EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition & Center for Innovative Medicine
Halsovagen 7, SE-141 83 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jovine at ki.se<mailto:luca.jovine at ki.se>
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On 27 Apr 2015, at 10:52, Tristan Croll <tristan.croll at qut.edu.au<mailto:tristan.croll at qut.edu.au>> wrote:


I'm currently using the dev 2000 version of Phenix, and noticed an issue with the automatic linking of N-linked (and presumably O-linked) glycans. If you feed a glycosylated structure sans hydrogens to Phenix and allow ReadySet to add hydrogens prior to refinement, it adds hydrogens as if the glycans are unlinked. Then, the automatic linking script rejects them due to valence issues.


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