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Hi Joe,<br>
<br>
hm... it's getting a bit complicated. Could you please send me the
PDB file (or its part containing the residue in question plus a
couple of residues on both ends)? I need to reproduce this problem
myself to be able to explain what's happening and how to deal with
this.<br>
<br>
I guess you need to import a CIF file for modified residues into
COOT so it can rotate about torsions.<br>
<br>
Thanks!<br>
Pavel.<br>
<br>
<br>
On 8/13/10 11:26 AM, Joseph Noel wrote:
<blockquote cite="mid:AD05B4A2-A378-48AE-AB83-087FA16A53F8@salk.edu"
type="cite">Thanks all for the advice. Basically that is what I
have been doing. It is actually an oxidized cysteine to sulfenic
acid. I am refining the site as alternative conformers with the
normal Cys, the single oxidation state to sulfenic acid (CSO) and
the double to sulfinic acid (CSD). I know that CSO is in the
phenix library but it adds hydrogens to the amino group every time
I run elbow or ready set. I then I have to edit the PDB file to
delete the hydrogen or Phenix will not refine. I also have
problems in COOT. It will not let me move the residues torsional
angles. I have checked other structures in the PDB and the density
fits perfectly with the structures of many such oxidized systems
but for some reason Phenix is giving me some problems. I was going
to create a "new" residue and explicitly define the oxygen as
charged rather then protonated since the pKa of sulfenic acid is
quite low. Maybe the problems all stem from refining this
particular position with three alternative "conformers", each
conformer of which is chemically distinct. For now, I have CSO
labeled as convention BCSO for conformer B. Cys is ACYS.
<div><br>
</div>
<div>Joe<br>
<div>
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<div style="word-wrap: break-word;">___________________________________________________________</div>
<div style="word-wrap: break-word;">Joseph P. Noel, Ph.D.<br>
Investigator, Howard Hughes Medical Institute<br>
Professor, The Jack H. Skirball Center for Chemical
Biology and Proteomics<br>
The Salk Institute for Biological Studies<br>
10010 North Torrey Pines Road<br>
La Jolla, CA 92037 USA<br>
<br>
Phone: (858) 453-4100 extension 1442<br>
Cell: (858) 349-4700<br>
Fax: (858) 597-0855<br>
E-mail: <a moz-do-not-send="true"
href="mailto:noel@salk.edu">noel@salk.edu</a><br>
<br>
Web Site (Salk): <a moz-do-not-send="true"
href="http://www.salk.edu/faculty/faculty_details.php?id=37">http://www.salk.edu/faculty/faculty_details.php?id=37</a><br>
Web Site (HHMI): <a moz-do-not-send="true"
href="http://hhmi.org/research/investigators/noel.html">http://hhmi.org/research/investigators/noel.html</a><br>
___________________________________________________________<br>
</div>
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<br>
</div>
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