[phenixbb] O-linked glycosylation refinement in Phenix

Nigel Moriarty nwmoriarty at lbl.gov
Mon Apr 11 15:19:13 PDT 2011


Did you get my email about this?

On Mon, Apr 11, 2011 at 2:15 PM, Qiang Chen <chen at red.dfci.harvard.edu> wrote:
> Dear all,
>
> I'm refining a structure which has both N-linked and O-linked
> glycosylation. I use Phenix to do the refinement. It works well for the
> N-linked NAG. I defined the link as the following:
>
>    apply_cif_link {
>      data_link = "NAG-ASN"
>      residue_selection_1 = "chain A and resname NAG and resid 701"
>      residue_selection_2 = "chain A and resname ASN and resid 518"
>    }
>
> But it doesn't work when I defined the fucose-threonine link as the
> similar way:
>
>    apply_cif_link {
>      data_link = "FUC-THR"
>      residue_selection_1 = "chain A and resname FUC and resid 801"
>      residue_selection_2 = "chain A and resname THR and resid 596"
>    }
>
> The error message is "missing CIF link: data_link_FUC-THR".
>
> Does anyone have the cif link file of FUC-THR?
>
> Thanks a lot!
>
>
> Qiang
>
>
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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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