[phenixbb] apply_cif_link

[Engin Ozkan]

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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-- 
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111