<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
I agree with Pavel. Disulfides are hit by radiation damage, and I
usually observe "partially reduced" disulfides in datasets I collect
at synchrotrons. If that is the case, the solution is to create
alternate conformations for the cysteines involved. Make sure the
reduced cysteines have the same altloc, and are moved into positive
mFoFc density, so that Phenix does not automatically link them as
disulfides.<br>
<br>
Engin<br>
<br>
<div class="moz-cite-prefix">On 2/15/16 2:46 AM, Pavel Afonine
wrote:<br>
</div>
<blockquote cite="mid:56C19060.8040306@lbl.gov" type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
P.S.: <br>
<br>
<div class="moz-cite-prefix">If atom is misplaced normally you
would see both: positive and negative residual density in close
proximity to each other. <br>
<br>
If you only see negative density at SG centers this may mean the
site is partially occupied.<br>
<br>
Pavel<br>
<br>
</div>
<blockquote
cite="mid:368539498.3207258.1455485080089.JavaMail.yahoo@mail.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
<div id="yui_3_16_0_1_1455483927872_4897" dir="ltr">Sorry, my
previous email was incomplete. My structure has negative
density in the center of some disulfides (the magnitude of
this effect vary between different monomers in the ASU). I'd
like to refine the structure in an "artificial reduced
form", where cysteines involved in disulfides are treated in
reduced form, but repulsions originating from neighboring
sulfur atoms are turned-off, to monitor distances (I expect
that SG atoms remain close to 2 A), guided only by data.
Thank you,<br>
</div>
<br>
</div>
</blockquote>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
Unsubscribe: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a></pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">
</pre>
</body>
</html>