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To add to this: best way to generate restraints file within Phenix
framework is to use eLBOW with a SMILES string (using GUI or CL),
then quickly inspect the restraints file (aka 'ligand CIF file') to
make sure it reflects what you know about the ligand.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 1/8/21 08:02, Maxime Cuypers wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CACT_3tE0Oz8FTC6VGTY4_VBA_iu8njw8m37s8npmsJ4d7kxy2A@mail.gmail.com">
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<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"
moz-do-not-send="true">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" moz-do-not-send="true">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>
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