[phenixbb] Sugar woes

Simon Kolstoe s.kolstoe at ucl.ac.uk
Tue Apr 17 03:18:57 PDT 2012

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
  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?



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