On Wed, Aug 4, 2010 at 10:43 AM, Joseph Noel <span dir="ltr">&lt;<a href="mailto:noel@salk.edu">noel@salk.edu</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;">

Thanks Pavel! I will wait and see what Ralf says regarding defining the symmetry operator. If I am using the GUI for phenix.refine should I create a new file with the bond definition you mention and include it as one of the starting files or should I edit the Refine_*.eff file that gets created and insert it somewhere there?<br>

</blockquote><div><br></div><div>Either of these should work, but there is also a third option: open Settings menu, select &quot;Geometry restraints&quot;, then &quot;Edit geometry restraints&quot;, and define custom bonds there.  (FYI, if you&#39;re going to edit the .eff file directly, you want to select &quot;Edit parameters and run&quot; when clicking the run button - not sure if that&#39;s what you meant, but other methods involving the GUI tend to not work, which has been a source of confusion for some command-line users.)</div>

<div><br></div><div>-Nat</div></div>