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
1001
atom_selection_2 = name OG1 and chain A and resname THR and resseq
100
distance_ideal = 1.439
sigma = 0.050
}
}
The above generates a generic covalent bond between C1 of NGA and OG1 of
THR.
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
restraints:
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 .
bond_NAG-C1_=_THR-OG1
######
and
######
data_link_NAG-THR
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
NAG-THR 1 C1 2 OG1 single 1.439 .020
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
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.
Zhijie
-----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
Hello!
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?
Regards,
Cory
Cory Brooks,Ph.D.
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