[phenixbb] Glycan refinement

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Nov 10 11:14:15 PST 2009

> I am refining a structure with a N-linked glycosylation site. There
> is density that goes beyond the first NAG, at least to MAN3. I know
> in Phenix there is  data_link = NAG-ASN for the ASN-NAG connection,
> but I don't know how to do the "apply_cif_link' for the extensions
> such NAG-NAG, NAG-MAN, MAN-MAN...., any suggestions are appreciated.

Search in the mon_lib_list.cif file for "data_link_ALPHA" and
"data_link_BETA" to find the links you need, then specify them
in additional apply_cif_link blocks, one for each link.

The command


will give you the location of the mon_lib_list.cif file.
Let me know if you cannot find all the links you need.

Reports about the links should appear in the phenix.refine log.
You can check in the .geo file if all restraints were built


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