Grant You have two atoms in your PDB named differently from the restraints file you are using for NGA. You need to reconcile the differences. The standard naming does not include O and O1L. I would recommend editing your PDB to match the restraints file. Nigel 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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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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