<div dir="ltr">Please send me the file directly.</div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Thu, Jul 28, 2016 at 5:52 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<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><span class="HOEnZb"><font color="#888888">
<p><br>
</p>
<p>Pavel</p></font></span><span class="">
<p><br>
</p>
<br>
<div>On 7/28/16 05:39, Amber Lee wrote:<br>
</div>
<blockquote type="cite">
<div style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<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>
</div>
</blockquote>
<br>
</span></div>
<br>_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a><br></blockquote></div><br></div>