On Tue, Jun 22, 2010 at 2:56 PM, Scott Classen <span dir="ltr">&lt;<a href="mailto:sclassen@lbl.gov">sclassen@lbl.gov</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I set main.secondary_structure_restraints = True<br>
and it appears that protein ss elements are found and added to the geo file, but watson crick pairs are not.<br><br>
My DNA looks like this:<br>
<br>
HETATM    1  O5*  Ad D   1     -47.740 -49.121 -17.972  1.00 91.44           O<br>
ANISOU    1  O5*  Ad D   1    13002   6701  15042   3404   -258  -1747       O<br><br>
Is there any reason it wouldn&#39;t be recognized by PROBE?<br></blockquote><div><br></div><div>Jeff says that PROBE probably won&#39;t recognize &quot;Ad&quot; (it expects &quot;dA&quot; instead), and the default behavior probably requires O5&#39;, not O5*.  The atom naming we can probably work around, the residue names are more difficult.  What program generated these residues?</div>
<div><br></div><div>If you can send us the model (or just enough of it to have base pairs, actually), we&#39;ll take a look.</div><div><br></div><div>-Nat</div></div>