Hi Yarrow,<div><br></div><div>Try:</div><div><br></div><div>phenix.elbow --smiles &#39;[C-]#[O+]&#39;</div><div><br></div><div>(The smiles string is from the wikipedia page on carbon monoxide.)</div><div><br></div><div>Ralf<br>
<br><div class="gmail_quote">On Fri, Jul 8, 2011 at 10:41 AM, Yarrow Madrona <span dir="ltr">&lt;<a href="mailto:amadrona@uci.edu">amadrona@uci.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Hi,<br>
<br>
I am trying to use Elbow and smiles to generate carbon monoxide<br>
coordinates. I thought it would be easy enough. I made two waters in coot<br>
and changed the the oxygens to C and O and set the distance around 1.13<br>
angstrom.  Saved these coordinates as a PDB. I then used this in Elbow but<br>
it gives me a methyl group.  Not sure what is going on. Any help would be<br>
appreciated. Thank you!<br>
<br>
-Yarrow<br>
<br>
--<br>
Yarrow Madrona<br>
<br>
Graduate Student<br>
Molecular Biology and Biochemistry Dept.<br>
University of California, Irvine<br>
Natural Sciences I, Rm 2403<br>
Irvine, CA 92697<br>
<br>
<br>
<br>
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</blockquote></div><br></div>