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

Tristan Croll tristan.croll at qut.edu.au
Mon Apr 27 13:53:24 PDT 2015

Actually, the situation is more complex. If I use 4fxk downloaded straight from the PDB, the parser in phenix.link_edits fails to find the  LINK records, leading to phenix.ready_set incorrectly adding hydrogens. If, however, I take the same file and strip it back to the bare minimum (CRYST, LINK and ATOM cards) it works fine.

Tristan Croll
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On 27 Apr 2015, at 7:01 pm, Luca Jovine <Luca.Jovine at ki.se<mailto:Luca.Jovine at ki.se>> wrote:

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.
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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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