Morten<div><br></div><div>It is always best not to use the PDB format as input if another is available as it suffers from a number of limitations. However, I am surprised that the other formats didn&#39;t provide a better result. I&#39;d be interested in the 3 files you downloaded.</div>

<div><br></div><div>To solve your problem, one of the best ways to get restraints is with the help of the Chemical Components. Your ligand, CYM, is specified by the PDB and you can use eLBOW to create a restraints file.</div>

<div><br></div><div>phenix.elbow --chemical-component=cym</div><div><br></div><div>and its available in the GUI also.</div><div><br></div><div>Cheers</div><div><br></div><div>Nigel</div><div><br><div class="gmail_quote">
On Tue, Mar 5, 2013 at 6:16 AM, Morten Groftehauge <span dir="ltr">&lt;<a href="mailto:mortengroftehauge.work@gmail.com" target="_blank">mortengroftehauge.work@gmail.com</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Bump.<div><br></div><div>I have an S-methylcysteine sulfoxide so I downloaded it from WebCSD from the CCDC website. So far so good. Available in three formats but I wanted it to work as a modified residue so I followed the advice here. Opened it in PyMol, saved it as a pdb file and edited the atoms in a text editor to fit with a normal residue. But phenix.elbow doesn&#39;t treat sulfur correctly. The geometry is right but it adds an extra hydrogen to the sulfur and the oxygen - they should have a double bond instead. If I run phenix.elbow directly on the files downloaded from WebCSD I get the double bond but I also get a flat system; as if my sulfur was a carbon.</div>


<div>Yes, I tried --opt.</div><div>Attached the best results.</div><div>My phenix version is 1299.</div><div><br></div><div>tl;dr phenix.elbow fails at parameterising DMSO.</div><div><br>
</div><div>Help?</div><div><br></div><div>Cheers,</div><div>Morten</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On 29 July 2012 04:41, Paul Emsley <span dir="ltr">&lt;<a href="mailto:paul.emsley@bioch.ox.ac.uk" target="_blank">paul.emsley@bioch.ox.ac.uk</a>&gt;</span> wrote:<br>


</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
  
    
  
  <div text="#000000" bgcolor="#FFFFFF"><div>
    <div>On 27/07/12 13:43, Schubert, Carsten
      [JRDUS] wrote:<br>
    </div>
    <blockquote type="cite">
      
      
      
      <div>
        <div>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">What
              are the current best practices for modified aminoacids? I
              have a peptide with and N-terminal Acetyl-proline which I
              am trying to model. The initial approach was to locate the
              aminoacid in the chemical components dictionary (N7P) and
              replace the residue in coot. </span></p>
        </div>
      </div>
    </blockquote>
    <br></div>
    do the restraints specify that N7P is a non-polymer (in which case
    coot will treat it as such) or as an L-peptide? <br><div>
    <br>
    <blockquote type="cite">
      <div>
        <div>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">Unfortunately
              the link to the next residue is not recognized, so the
              residue is just floating about. </span></p>
        </div>
      </div>
    </blockquote>
    <br></div>
    Doesn&#39;t sound very much like how a L-peptide should behave to me...<span><font color="#888888"><br>
    <br>
    Paul.<br>
    <br>
  </font></span></div>

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<br></div></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br>Morten K Grøftehauge, PhD <div>Pohl Group</div><div>Durham University</div>
</font></span></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709     Email : NWMoriarty@LBL.gov<br>

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