Are you talking about the &quot;auto fit rotamer&quot; function? I am not using that. I tend to select rotamers from the list but I rarely pic the auto one (it tends to place my side chains inside the neighbouring main chain densities most of the time). <div>
<br></div><div>Mario Sanches<br><br><div class="gmail_quote">On Thu, Apr 19, 2012 at 9:06 AM, Nathaniel Echols <span dir="ltr">&lt;<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On Thu, Apr 19, 2012 at 8:00 AM, Mario Sanches &lt;<a href="mailto:mariosan@gmail.com">mariosan@gmail.com</a>&gt; wrote:<br>
&gt; I see regions with bad clashes solely because during refinement a side chain<br>
&gt; is being fit into a density peak that is to close to another residue atoms.<br>
&gt; I wonder if there is a way to tell the program to avoid clashes even if it<br>
&gt; is at the expense of real-space fitting?<br>
<br>
</div>Are you using the automatic rotamer correction?  This performs poorly<br>
at low resolution - 2.9A is about the point where it really breaks<br>
down.<br>
<div class="HOEnZb"><div class="h5"><br>
-Nat<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Mario Sanches<br>Postdoctoral Researcher<br>Samuel Lunenfeld Research Institute<br>Mount Sinai Hospital<br>600 University Ave<br>Toronto - Ontario<br>
Canada<br>M5G 1X5<br><a href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
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