So how do people deal with this? I would think close cysteines are fairly common in metal coordination sites.<br><br>Ursula<br><br><div class="gmail_quote">On Thu, Jun 27, 2013 at 7:12 AM, Nathaniel Echols <span dir="ltr">&lt;<a href="mailto:nechols@lbl.gov" target="_blank">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 Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine &lt;<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>&gt; wrote:<br>

&gt; Hm.. this isn&#39;t easy.. phenix.refine automatically identifies disulfide<br>
&gt; bonds and creates restrains for them. This is controlled by<br>
&gt; disulfide_distance_cutoff=3 parameter. You can set it to some big number, so<br>
&gt; none desulfide bonds will be created automatically<br>
<br>
</div>Are you sure it&#39;s not the reverse?  I think this number sets the<br>
maximum distance allowed for disulfides; increasing it will just bond<br>
more distant atoms.<br>
<br>
-Nat<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Ursula Schulze-Gahmen, Ph.D.<br>Assistant Researcher<br>UC Berkeley, QB3<br>356 Stanley Hall #3220<br>Berkeley, CA 94720-3220<br>