[phenixbb] Refinement and glycosylation.

Nigel Moriarty nwmoriarty at lbl.gov
Mon Dec 10 11:38:01 PST 2012


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

Are you asking how to link two carbohydrate units?

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



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

On Mon, Dec 10, 2012 at 7:41 AM, Jan van Agthoven <janccp4 at gmail.com> 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,
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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