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Grant<br>
<br>
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.<br>
<br>
Nigel<br>
<br>
On 4/23/10 11:53 AM, Hansman, Grant (NIH/VRC) [F] wrote:
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<div class="Section1">
<p class="MsoNormal">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. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">For , example, I am using this:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">refinement.pdb_interpretation {<o:p></o:p></p>
<p class="MsoNormal"> apply_cif_link {<o:p></o:p></p>
<p class="MsoNormal"> data_link = BETA1-2<o:p></o:p></p>
<p class="MsoNormal"> residue_selection_1 = chain C and resname
GAL and resid 224<o:p></o:p></p>
<p class="MsoNormal"> residue_selection_2 = chain C and resname
FUC and resid 223<o:p></o:p></p>
<p class="MsoNormal"> }<o:p></o:p></p>
<p class="MsoNormal"> apply_cif_link {<o:p></o:p></p>
<p class="MsoNormal"> data_link = BETA1-3<o:p></o:p></p>
<p class="MsoNormal"> residue_selection_1 = chain C and resname
GAL and resid 224<o:p></o:p></p>
<p class="MsoNormal"> residue_selection_2 = chain C and resname
NGA and resid 225<o:p></o:p></p>
<p class="MsoNormal"> }<o:p></o:p></p>
<p class="MsoNormal"> apply_cif_link {<o:p></o:p></p>
<p class="MsoNormal"> data_link = BETA1-3<o:p></o:p></p>
<p class="MsoNormal"> residue_selection_1 = chain C and resname
NGA and resid 225<o:p></o:p></p>
<p class="MsoNormal"> residue_selection_2 = chain C and resname
FUC and resid 226<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> Number of atoms: 46<o:p></o:p></p>
<p class="MsoNormal"> Number of conformers: 1<o:p></o:p></p>
<p class="MsoNormal"> Conformer: ""<o:p></o:p></p>
<p class="MsoNormal"> Number of
residues, atoms: 4, 46<o:p></o:p></p>
<p class="MsoNormal">
Unusual residues: {'GAL%DEL-HO2%DEL-HO3': 1, 'NGA%DEL-O1%DEL-HO3': 1,
'FUC%DEL-O1': 2}<o:p></o:p></p>
<p class="MsoNormal">
Unexpected atoms: {'NGA%DEL-O1%DEL-HO3,O1L': 1, 'NGA%DEL-O1%DEL-HO3,O':
1}<o:p></o:p></p>
<p class="MsoNormal">
Classifications: {'undetermined': 4}<o:p></o:p></p>
<p class="MsoNormal">
Modifications used: {'DEL-HO2': 1, 'DEL-HO3': 2, 'DEL-O1': 3}<o:p></o:p></p>
<p class="MsoNormal"> Link
IDs: {None: 3}<o:p></o:p></p>
<p class="MsoNormal">
Unresolved non-hydrogen bonds: 3<o:p></o:p></p>
<p class="MsoNormal">
Unresolved non-hydrogen angles: 6<o:p></o:p></p>
<p class="MsoNormal">
Unresolved non-hydrogen dihedrals: 4<o:p></o:p></p>
<p class="MsoNormal">
Unresolved non-hydrogen chiralities: 2<o:p></o:p></p>
<p class="MsoNormal">
Unresolved apply_cif_link angles: 1<o:p></o:p></p>
<p class="MsoNormal">
Unresolved apply_cif_link chiralities: 1<o:p></o:p></p>
<p class="MsoNormal"> Number of atoms with unknown nonbonded energy
type
symbols: 2<o:p></o:p></p>
<p class="MsoNormal"> "HETATM 5649 O NGA
C 225 .*. O "<o:p></o:p></p>
<p class="MsoNormal"> "HETATM 5655 O1L NGA C 225
.*. O "<o:p></o:p></p>
<p class="MsoNormal"> Time building chain proxies: 2.31, per 1000
atoms:
0.41<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sorry: Fatal problems interpreting PDB file:<o:p></o:p></p>
<p class="MsoNormal"> Number of atoms with unknown nonbonded energy
type
symbols: 2<o:p></o:p></p>
<p class="MsoNormal"> Please edit the PDB file to resolve the
problems
and/or supply a<o:p></o:p></p>
<p class="MsoNormal"> CIF file with matching restraint definitions,
along
with<o:p></o:p></p>
<p class="MsoNormal"> apply_cif_modification and apply_cif_link
parameter
definitions<o:p></o:p></p>
<p class="MsoNormal"> if necessary (see phenix.refine documentation).<o:p></o:p></p>
<p class="MsoNormal"> Also note that phenix.elbow is available to
create
restraint<o:p></o:p></p>
<p class="MsoNormal"> definitions for unknown ligands.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any help and direction would be appreciated.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Grant<o:p></o:p></p>
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<pre wrap="">
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<pre class="moz-signature" cols="72">--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Fax : 510-486-5909 Web : CCI.LBL.gov</pre>
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