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