Jan

NAG is the beta form. NDG is the alpha form. You may have an incorrect geometry.

Are you asking how to link two carbohydrate units?

If you can send me the model.pdb I will take a look.

Cheers

Nigel

NB. Any files sent to me will be held in strictest confidence.

On Mon, Dec 10, 2012 at 7:41 AM, Jan van Agthoven <[email protected]> wrote:

Hi everyone,
I refined my structure using phenix.refine and used the following
parameters to define the ASN-NAG link:
refinement.pdb_interpretation.apply_cif_link {
  data_link = NAG-ASN
  residue_selection_1 = chain A and resname NAG and resseq  x
  residue_selection_2 = chain A and resname ASN and resseq   y
}

However I would like the glycosylation to be Beta (NAG in Beta configuration).
How can I define this in the parameter file?
Thanks,
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Nigel W. Moriarty
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