[phenixbb] definition of glycosylation in phenix.refine

[Laurent Maveyraud]

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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Laurent Maveyraud         laurent.maveyraud AT ipbs DOT fr
P I C T   ---  Plateforme Intégrée de Criblage de Toulouse
Université  Paul  Sabatier /  CNRS  /  I.P.B.S.  UMR  5089
Département     Biologie    Structurale   et   Biophysique
http://cribligand.ipbs.fr               http://www.ipbs.fr
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