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<p>Hi,</p>
<p><br>
</p>
<p>sounds like a bug. Could you please send me PDB file (please send
to me directly, not entire mailing list)?</p>
<p><br>
</p>
<p>Meanwhile, a quick work-around is to use link_ligands=False (if
you are using command line) or if using the GUI:</p>
<p><br>
</p>
<p>Refinement settings -> Automatic linking options -> uncheck
"Link ligands to protein" .</p>
<p><br>
</p>
<p>Pavel</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 7/28/16 05:39, Amber Lee wrote:<br>
</div>
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<p>Dear all, Dear Pavel,</p>
<p><br>
</p>
<p>I have encountered a problem where a new bond was generated
between the O of SO4 and O(H) of my ligand (with a glycerol
head group, I call it glycerol here).
<br>
</p>
<p><br>
</p>
<p>As shown in the figure in the Dropbox link below, I have
placed the glycerol (purple) in the density and it fits well.
The distance between the O of SO4 and the OH of glycerol was
2.55 angstrom. After refinement (yellow) however, the glycerol
was pulled out of density with the distance changed to 1.27
angstrom, therefore forming a new bond.
<br>
</p>
<p><br>
</p>
<p>When hydrogens were added to the glycerol,�the glycerol was
again pulled, forming a C-O bond between SO4 and glycerol.�
<br>
</p>
<p><br>
</p>
<p>When the positions (xyz) of the glycerol atoms were fixed,
the SO4 was pulled towards glycerol, making a O-O bond between
SO4 and glycerol.
<br>
</p>
<p><br>
</p>
<p><span>When the positions of the SO4 and glycerol were both
fixed during the refinement, the result came out saying the
bond length was too long between the the O (SO4) and the O
(glycerol).
<br>
</span></p>
<p><span><br>
</span></p>
<p><span><span>Thus I thought Phenix must treated it as a
covalent bond. </span></span><br>
</p>
<p><br>
</p>
<p>I have tried Rafmac and it did not do this to the model. The
cif files etc were the same for Phenix and Rafmac.</p>
<p><br>
</p>
<p>The problem appeared both on version 1.10-2152 and the latest
version 1.10.2155.</p>
<p><br>
</p>
<p>How could I fix this problem?</p>
<p><br>
</p>
<p>Many thanks,</p>
<p><br>
</p>
<p>Jingyi Hu<br>
</p>
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