<div dir="auto">Hello,<div dir="auto">Naively, Perhaps the issue is that the molecule used to generate the .cif restraints does not have the hydrogens in the right place/ right hybridization? </div><div dir="auto">My suggestion would be to check it i.e. with Avogadro or any other chemical structure editor.</div><div dir="auto"><br></div><div dir="auto">Cheers</div><div dir="auto">Maxime</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le jeu. 7 janv. 2021 à 14:04, Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
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 href="http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10" target="_blank" rel="noreferrer">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>On 1/7/21 10:20, Sharan Karade wrote:<br>
</div>
<blockquote type="cite">
<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>
<div dir="ltr" data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>Sharan Karade<br>
Postdoc-fellow</div>
<div>IBBR-UMD, <span>9600 Gudelsky Dr, </span></div>
<div>Rockville</div>
<div>Maryland 20850<br>
<br>
<br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
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