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Hi Melissa,<br>
<br>
we need to have a closer look to understand what's happening...<br>
<br>
Could you please send us these PDB file:<br>
- original (before modifications);<br>
- file after modifications;<br>
- file after refinement;<br>
- cif file.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 1/11/17 14:15, Melissa Ford wrote:<br>
</div>
<blockquote
cite="mid:AEE3C229-6B5D-4809-8B34-27F477520164@gmail.com"
type="cite">
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charset=windows-1252">
<font class="" face="calibri, arial, helvetica, sans-serif"
size="3">I'm having working on modeling a sulfur on the
phosphate backbone of DNA in replace of one of the oxygens and
have encountered some restraint problems. I've successfully
managed to replace the oxygen with a sulfur in the proper
geometry in a pdb, generate a cif file for the modified residue
(adenosine 5'-phosphorothioate), and run an initial refinement.
Upon that refinement, a few errors occur. First, since the
phosphate bound to the sulfur is the first atom of the modified
residue the angle between the O3' (of the neighboring residue) -
P- S is not recognized and forced into an unfavorable geometry.
When trying to add that additional angle to the cif�file, I get
an error. Aditionally, the change causes Phenix to not recognize
the chirality of the C3' that the phosphate is bonded to and
forces the ribose into a planar conformation.�I am sure there is
something I am�missing that allows phenix to recognize this new
residue as a modified nucleotide so that it knows these
restraints.�Any insight on this would be great. Thank you!�</font>
</blockquote>
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