Your problem might be because your definition of NGA (I hope you are adding an NGA.cif, the phenix monomer library does not have a full geometry description file) matches exactly the NGA you have in your PDB. If they don't, modify atom names so they match perfectly. There are a few ways you can do it, I guess. The easiest might be to get both the PDB and the cif library file from HIC-UP/PRODRG. Or just look in your pdb and read your cif file. The solution might be obvious, then. Engin P.S. What is NGA? Is it N-acetyl-D-glucosamine or N-acetyl-D-galactosamine? For some reason, in the mon_lib_list.cif (1.6.1), there is a line that says NAG-b-D (N-acetyl-D-glucosamine) is a synonym for NGA, but then below NGA is called N-acetyl-D-galactosamine. Could this be an error in the monomer library? On 4/23/10 11:53 AM, Hansman, Grant (NIH/VRC) [F] wrote:
I am trying to link my sugar molecule (FUC-GAL-NGA-FUC), Lewis y, for phenix.refine, but I keep on getting an error message. I am a beginner at this so I just don’t know how to make the links.
For , example, I am using this:
refinement.pdb_interpretation {
apply_cif_link {
data_link = BETA1-2
residue_selection_1 = chain C and resname GAL and resid 224
residue_selection_2 = chain C and resname FUC and resid 223
}
apply_cif_link {
data_link = BETA1-3
residue_selection_1 = chain C and resname GAL and resid 224
residue_selection_2 = chain C and resname NGA and resid 225
}
apply_cif_link {
data_link = BETA1-3
residue_selection_1 = chain C and resname NGA and resid 225
residue_selection_2 = chain C and resname FUC and resid 226
Number of atoms: 46
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 46
Unusual residues: {'GAL%DEL-HO2%DEL-HO3': 1, 'NGA%DEL-O1%DEL-HO3': 1, 'FUC%DEL-O1': 2}
Unexpected atoms: {'NGA%DEL-O1%DEL-HO3,O1L': 1, 'NGA%DEL-O1%DEL-HO3,O': 1}
Classifications: {'undetermined': 4}
Modifications used: {'DEL-HO2': 1, 'DEL-HO3': 2, 'DEL-O1': 3}
Link IDs: {None: 3}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 4
Unresolved non-hydrogen chiralities: 2
Unresolved apply_cif_link angles: 1
Unresolved apply_cif_link chiralities: 1
Number of atoms with unknown nonbonded energy type symbols: 2
"HETATM 5649 O NGA C 225 .*. O "
"HETATM 5655 O1L NGA C 225 .*. O "
Time building chain proxies: 2.31, per 1000 atoms: 0.41
Sorry: Fatal problems interpreting PDB file:
Number of atoms with unknown nonbonded energy type symbols: 2
Please edit the PDB file to resolve the problems and/or supply a
CIF file with matching restraint definitions, along with
apply_cif_modification and apply_cif_link parameter definitions
if necessary (see phenix.refine documentation).
Also note that phenix.elbow is available to create restraint
definitions for unknown ligands.
Any help and direction would be appreciated.
Grant
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