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Hi Sharan,<br>
<br>
I'm guessing your are over-relying on graphic representations of
your molecules which is discussed here to some extent:<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10">http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10</a><br>
<br>
What really matters is that the ligand fits the map and its geometry
matches what's expected. <br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 1/7/21 10:20, Sharan Karade wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CANuTR8nGGjG4+60Fzfzcmn=vwO_p7UQ4be0L7Og7Q3FsBzBidw@mail.gmail.com">
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<div dir="ltr">Hello all,
<div><br>
</div>
<div>I hope everybody is doing well. Happy New Year 2021!!!</div>
<div><br>
</div>
<div> I am stuck with some unusual behavior of restrain files
generated by Phenix.ReadySet. I crystallized the protein with
ligands which have double bonds between the atoms. As I see
clear electron density for the ligand, I drew a ligand
molecule in Coot (Ligand builder) and fitted in electron
density very nicely. Until here, I can see the double bonds in
the modelled ligand. I generated the restrain files using
Phenix.ReadySet to further proceed for refinement.
Unfortunately, after refinement the double bonds were
converted to single bonds. I tried to generate new
restrain files and refined the model, resulting in similar
output. But, fortunately in one case, the double bonds were
retained after refinement also. I tried to repeat with other
ligands, where I was unsuccessful to retain the double bonds.</div>
<div><br>
</div>
<div>please help me. Thank you so much. </div>
<div><br>
</div>
<div>Regards</div>
<div>Sharan</div>
<div>
<div><br>
</div>
-- <br>
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<div>Sharan Karade<br>
Postdoc-fellow</div>
<div>IBBR-UMD, <span>9600 Gudelsky Dr, </span></div>
<div>Rockville</div>
<div>Maryland 20850<br>
<br>
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