[phenixbb] O-linked glycosylation refinement in Phenix

Pavel Afonine pafonine at lbl.gov
Mon Apr 11 21:41:47 PDT 2011


Hi Qiang,

although apply_cif_link is probably more elegant way of doing this, you 
can always use custom bonds (if you can't get apply_cif_link to work):

http://phenix-online.org/documentation/refinement.htm#anch86

Using custom bonds you can define a covalent bond between any two atoms.

For example, this

refinement.geometry_restraints.edits {
     bond {
       atom_selection_1 = chain A and resseq 17 and name O
       atom_selection_2 = chain B and resseq 18 and name N
       distance_ideal = 1.5
       sigma = 0.02
     }
}

will define a bond between these two atoms

HETATM  115  O   LIG A  17       3.129  18.483   4.947  1.00 
44.08           O
HETATM  116  N   LIG B  18      -2.025   7.355   5.786  1.00 
33.96           N

You can define any number of such bonds by duplicating bond {} scope of 
parameters. You can define angle as well.

Check .geo  file to see if atoms in question are bonded.

Pavel.


On 4/11/11 2:15 PM, Qiang Chen 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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