[phenixbb] Link NGA and THR

Zhijie Li zhijie.li at utoronto.ca
Mon Apr 13 15:10:09 PDT 2015

Hi Cory,

Did you supply phenix with a "edits" file that indicates that there is a 
glycosidic bond between the Thr and the NGA? Such file is a simple text file 
with content like this:

refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = name  C1     and chain A and resname NGA and resseq 
    atom_selection_2 = name  OG1  and chain A and resname THR and resseq 
    distance_ideal = 1.439
    sigma = 0.050

The above generates a generic covalent bond between C1 of NGA and OG1 of 

Alternatively, you can use the NAG-THR link that is already in the standard 
monomer library. (Note that this is actually for GlcNAc-Thr, but it should 
work for NGA-Thr too. Yes, its a hack.) This way you get a few more 

refinement.pdb_interpretation.apply_cif_link {
data_link = NAG-THR
residue_selection_1 = chain A and resname NGA and resseq 1001
residue_selection_2 = chain A and resname THR  and resseq  100

Note the NAG and NGA.

For your reference, the NAG-THR link is defined in the monomer library as:

NAG-THR  .        DEL-O1   pyranose THR      DEL-HG1  .


NAG-THR  1 C1      2 OG1       single      1.439     .020
NAG-THR  1 C1      2 OG1     2 CB      108.700    3.000
NAG-THR  1 O5      1 C1      2 OG1     112.300    3.000

Good luck.


-----Original Message----- 
From: Cory Brooks
Sent: Monday, April 13, 2015 3:13 PM
To: phenixbb at phenix-online.org
Subject: [phenixbb] Link NGA and THR


I am refining a structure with O-link glycosylation (GalNAc linked to
Thr). Phenix seems to remove the link during refinement. Can anyone
suggest a solution that will maintain the bond during refinement?


Cory Brooks,Ph.D.

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