Hi phenixbb, Every couple of years I come to build a sugar chain into a protein structure and hope the process is less painful than last time, however it seems things still are not smooth yet! I'm trying to build a fairly standard sugar chain onto a protein and am encountering many problems. What I am doing is using coot to get the coordinates for each sugar using the "File-> Get monomer" option and then putting the appropriate link in my phenix.refine .def file after renumbering the sugars. For example: apply_cif_link { data_link = "BETA1-2" residue_selection_1 = chain Z and resname NAG and resid 5 residue_selection_2 = chain Z and resname MAN and resid 4 } apply_cif_link { data_link = "BETA1-4" residue_selection_1 = chain Z and resname GAL and resid 6 residue_selection_2 = chain Z and resname NAG and resid 5 } For some reason I keep getting the following error: --------------- Chain: "Z" Number of atoms: 220 Number of conformers: 1 Conformer: "" Sorry: Traceback (most recent call last): File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1042, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/cif_types.py", line 399, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/cif_types.py", line 316, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: HO2 apply_mod failure: pdbres="NAG Z 5 " segid="Z " comp id: NAG-b-D mod id: DEL-HO2 ------------------ I haven't deleted the hydrogens that came with the sugars so what I thought it was doing was trying to delete an atom that isn't there, however adding a dummy atom with the name HO2 didn't work - any ideas? Also it seems happy with BETA1-4 links but not ALPHA2-6 links? How do I specify this link? Thanks, Simon