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<p>Nigel, <br>
</p>
<p>I have the file.</p>
<p>Pavel<br>
</p>
<br>
<div class="moz-cite-prefix">On 7/29/16 06:37, Nigel Moriarty wrote:<br>
</div>
<blockquote
cite="mid:CANkP=2eV-iaqtWWWtsgyR9hKqq8yOAOVK=nCedMHT50M_qC48A@mail.gmail.com"
type="cite">
<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 :
<a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a
moz-do-not-send="true"
href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div>
</div>
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<br>
<div class="gmail_quote">On Thu, Jul 28, 2016 at 5:52 PM, Pavel
Afonine <span dir="ltr"><<a moz-do-not-send="true"
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">
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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>
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