<div dir="ltr">Bump.<div><br></div><div style>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'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 style>Yes, I tried --opt.</div><div style>Attached the best results.</div><div style>My phenix version is 1299.</div><div style><br></div><div style>tl;dr phenix.elbow fails at parameterising DMSO.</div><div style><br>
</div><div style>Help?</div><div style><br></div><div style>Cheers,</div><div style>Morten</div><div style><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 29 July 2012 04:41, Paul Emsley <span dir="ltr"><<a href="mailto:paul.emsley@bioch.ox.ac.uk" target="_blank">paul.emsley@bioch.ox.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"><div class="im">
<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:"Calibri","sans-serif";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 class="im">
<br>
<blockquote type="cite">
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";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't sound very much like how a L-peptide should behave to me...<span class="HOEnZb"><font color="#888888"><br>
<br>
Paul.<br>
<br>
</font></span></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Morten K Gr�ftehauge, PhD�<div>Pohl Group</div><div>Durham University</div>
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