<div dir="ltr"><div dir="ltr">Hi Pavel, and <font color="#000000">Maxime</font></div><div dir="ltr"><span style="color:rgb(136,136,136)"><br></span></div><div><font color="#000000">Thank you so much for your valuable suggestions. I will try to generate the restrain file as you suggested and re-run the refinement.</font></div><div><font color="#000000"><br></font></div><div><font color="#000000"><br></font></div><div><font color="#000000">Regards</font></div><div><font color="#000000">Sharan</font></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jan 8, 2021 at 1:16 PM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
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>On 1/8/21 08:02, Maxime Cuypers wrote:<br>
</div>
<blockquote type="cite">
<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" target="_blank">pafonine@lbl.gov</a>> a écrit :<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);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" rel="noreferrer" target="_blank">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">
<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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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="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>