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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