<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt"><div>Hi!<br><br>I was trying to fit my ligands into my model and density. And I have successfully fitted 2 ligands (same molecule) but my 3rd ligand is different molecule.<br>After fitting my 3rd ligand (with COOT) and merged it with my protein, II created a restraint file with:<br><br> phenix.elbow my_model_coot-0..pdb --do-all --output=all_ligands<br><br>It created all_ligand.cif, which I used for in my next refinement with Phenix (GUI). I supplied my density, model and the restraint file and run phenix.refine.<br>Unfortunatate I'm getting this error message when it starts to run phenix.refine and opening COOT window:<br>
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<ul><ul><p style="margin-bottom: 0in; font-weight: normal;" align="JUSTIFY"><font face="Liberation Serif, serif"><font style="font-size: 8pt;" size="1"><tt class="western"><font face="Liberation Serif, serif"><font style="font-size: 10pt;" size="2"><span style="text-decoration: none;">Sorry:
Fatal problems interpreting PDB file:
</span></font></font></tt></font></font></p><p style="margin-bottom: 0in; font-weight: normal;" align="JUSTIFY"><tt class="western"><span style="text-decoration: none;">
</span></tt><font face="Liberation Serif, serif"><font style="font-size: 8pt;" size="1"><tt class="western"><font face="Liberation Serif, serif"><font style="font-size: 10pt;" size="2"><span style="text-decoration: none;">Number
of atoms with unknown nonbonded energy type symbols: 1
</span></font></font></tt></font></font></p><p style="margin-bottom: 0in; font-weight: normal;" align="JUSTIFY"><tt class="western"><span style="text-decoration: none;">
</span></tt><font face="Liberation Serif, serif"><font style="font-size: 8pt;" size="1"><tt class="western"><font face="Liberation Serif, serif"><font style="font-size: 10pt;" size="2"><span style="text-decoration: none;">Please
edit the PDB file to resolve the problems and/or supply a
</span></font></font></tt></font></font></p><p style="margin-bottom: 0in; font-weight: normal;" align="JUSTIFY"><tt class="western"><span style="text-decoration: none;">
</span></tt><font face="Liberation Serif, serif"><font style="font-size: 8pt;" size="1"><tt class="western"><font face="Liberation Serif, serif"><font style="font-size: 10pt;" size="2"><span style="text-decoration: none;">CIF
file with matching restraint definitions, along with
</span></font></font></tt></font></font></p><p style="margin-bottom: 0in; font-weight: normal;" align="JUSTIFY"><tt class="western"><span style="text-decoration: none;">
</span></tt><font face="Liberation Serif, serif"><font style="font-size: 8pt;" size="1"><tt class="western"><font face="Liberation Serif, serif"><font style="font-size: 10pt;" size="2"><span style="text-decoration: none;">apply_cif_modification
and apply_cif_link parameter definitions
</span></font></font></tt></font></font></p><p style="margin-bottom: 0in; font-weight: normal;" align="JUSTIFY"><tt class="western"><span style="text-decoration: none;">
</span></tt><font face="Liberation Serif, serif"><font style="font-size: 8pt;" size="1"><tt class="western"><font face="Liberation Serif, serif"><font style="font-size: 10pt;" size="2"><span style="text-decoration: none;">if
necessary (see phenix.refine documentation).
</span></font></font></tt></font></font></p><p style="margin-bottom: 0in; font-weight: normal;" align="JUSTIFY"><tt class="western"><span style="text-decoration: none;">
</span></tt><font face="Liberation Serif, serif"><font style="font-size: 8pt;" size="1"><tt class="western"><font face="Liberation Serif, serif"><font style="font-size: 10pt;" size="2"><span style="text-decoration: none;">Also
note that phenix.elbow is available to create restraint
</span></font></font></tt></font></font></p><p style="margin-bottom: 0in; font-weight: normal;" align="JUSTIFY"><tt class="western"><span style="text-decoration: none;">
</span></tt><font face="Liberation Serif, serif"><font style="font-size: 8pt;" size="1"><tt class="western"><font face="Liberation Serif, serif"><font style="font-size: 10pt;" size="2"><span style="text-decoration: none;">definitions
for unknown ligands.
</span></font></font></tt></font></font></p></ul></ul>
<br>I have use the same procedure for fitting my first 2 ligands. and it worked. But this time it failed!<br>What do you think I should do?<br><br><br>Thanks<br>Hermi<br><br><br></div>
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