[phenixbb] definition of glycosylation in phenix.refine
Engin Özkan
eozkan at uchicago.edu
Tue Nov 18 08:25:53 PST 2014
Hi Laurent,
If I am reading the error message right, you did not delete the
hydrogens that get removed upon bond formation. That's what it is
complaining about. I always thought Phenix probably removed these atoms
(the hydroxyl and the hydrogen) automatically when you defined the link,
but never tested if it really does it.
I also usually remove all hydrogens right away when sugar residues are
inserted.
Finally, I will recommend that you use automatic linking in the
phenix.refine GUI. It works great (I am on the latest nightly, dev-1839;
you may need to upgrade). No need to define pesky links anymore. Thank
you developers!
At the risk of hijacking the thread, I could not find in my installation
the cif files for N-linked sugars. Have they been moved elsewhere?
Hope this helps,
Engin
On 11/18/14 10:02 AM, Laurent Maveyraud wrote:
> Hi,
>
> I am currently refining a structure of a glycosylated protein, but I
> fail to define the appropriate links...
> The glycosylatin is
> Asn638-NAG1061-(beta1-4)-NAG1062-(beta1-4)-BMA1063-(ALPHA1-3)-MAN1064
>
> This is what I add in the eff file :
> apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain D and resname NAG and resid 1061
> residue_selection_2 = chain A and resname ASN and resid 638
> }
> apply_cif_link {
> data_link = BETA1-4
> residue_selection_1 = chain D and resname NAG and resid 1062
> residue_selection_2 = chain D and resname NAG and resid 1061
> }
> apply_cif_link {
> data_link = BETA1-4
> residue_selection_1 = chain D and resname BMA and resid 1063
> residue_selection_2 = chain D and resname NAG and resid 1062
> }
> apply_cif_link {
> data_link = ALPHA1-3
> residue_selection_1 = chain D and resname MAN and resid 1064
> residue_selection_2 = chain D and resname BMA and resid 1063
> }
> this is correctly read in refine:
> apply_cif_link:
> data_link: NAG-ASN
> mod_id_1: DEL-O1
> mod_id_2: DEL-HD22
> residue_selection_1: chain D and resname NAG and resid 1061
> residue_selection_2: chain A and resname ASN and resid 638
> apply_cif_link:
> data_link: BETA1-4
> mod_id_1: DEL-HO4
> mod_id_2: DEL-O1
> residue_selection_1: chain D and resname NAG and resid 1062
> residue_selection_2: chain D and resname NAG and resid 1061
> apply_cif_link:
> data_link: BETA1-4
> mod_id_1: DEL-HO4
> mod_id_2: DEL-O1
> residue_selection_1: chain D and resname BMA and resid 1063
> residue_selection_2: chain D and resname NAG and resid 1062
> apply_cif_link:
> data_link: ALPHA1-3
> mod_id_1: DEL-HO3
> mod_id_2: DEL-O1
> residue_selection_1: chain D and resname MAN and resid 1064
> residue_selection_2: chain D and resname BMA and resid 1063
> but generates an error :
>
> Number of atoms with unknown nonbonded energy type symbols: 5
> "HETATM10951 HO4 NAG D1052 .*. H "
> "HETATM10973 HO4 BMA D1053 .*. H "
> "HETATM11028 HO4 NAG D1062 .*. H "
> "HETATM11050 HO4 BMA D1063 .*. H "
> "HETATM11070 HO3 MAN D1064 .*. H "
>
> and the job stops.
>
> Any ideas on what if wrong ?
>
> thanks for your help
>
> Laurent
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