<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 &lt;<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>&gt; 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 &#39;ligand CIF file&#39;) 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 &lt;<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>&gt; 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&#39;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&#39;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>