[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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