<p>Hi all,</p>
<p>Fyi, many moons ago when I was building/refining 2iyb, I had to deactivate automatic disulphide detection to stop my metal sites from doing just this. This was refmac, so this problem is not confined to phenix.</p>
<p>Dave</p>
<div class="gmail_quote">On Jun 27, 2013 5:29 PM, "Pavel Afonine" <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Ursula,<br>
<br>
could you please send me the model and data files off list and
indicate unwanted S-S bonds? I may just implement automatic (or at
least easier than now) handling of this today or over the
week-end.<br>
<br>
Thanks,<br>
Pavel<br>
<br>
</div>
<blockquote type="cite">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"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine
<<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>>
wrote:<br>
> Hm.. this isn't easy.. phenix.refine automatically
identifies disulfide<br>
> bonds and creates restrains for them. This is
controlled by<br>
> disulfide_distance_cutoff=3 parameter. You can set it
to some big number, so<br>
> none desulfide bonds will be created automatically<br>
<br>
</div>
Are you sure it'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>
</blockquote>
</div>
</blockquote>
<br>
</div>
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