<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
</head>
<body text="#000000" bgcolor="#FFFFFF">
Hi Gyles,<br>
<br>
please send me files off list (model before and after refinement,
data and ligand cif if used; also indicate affected residues) and I
will investigate.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/16/19 04:13, Gyles Cozier wrote:<br>
</div>
<blockquote type="cite"
cite="mid:LO2P265MB055907DA36335B4F588081F6C8CE0@LO2P265MB0559.GBRP265.PROD.OUTLOOK.COM">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div id="divtagdefaultwrapper"
style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;"
dir="ltr">
<p style="margin-top:0;margin-bottom:0">Good afternoon,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I have been having
issues with the last 3 versions of Phenix (1.14, 1.15 and
1.16) when the XYZ(real-space) option is selected, version
1.13 was the last one that doesn't have this problem for me.
This seems to place too much weight on correcting rotamer
'outliers' at the expense of fitting to the density. The
proteins that I work on have always had some residues that
consistently are identified as rotamer outliers, but these
latest versions 'correct' just about all of them (typically
from 1% down to 0.1%). The resulting structures show clear
movement of the sidechains out of what should be their
density. Image 1 (after using 1.13) and 2 (after using 1.14,
1.15 or 1.16) show a really bad example where the Arg
sidechain even gets broken apart to be moved into the stronger
density of a neighbouring symmetry Gln.�<span>Image 3 (after
using 1.13) and 4 (after using 1.14, 1.15 or 1.16) is a more
subtle example, but although the residue is no longer a
rotamer outlier after refinement using 1.16, it clearly does
not fit the density as well as after using 1.13. These
subtle changes are particularly worrying, as they could
easily be missed when checking the structure after
refinement. Other members of the group have also noticed
this problem for different proteins.</span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span>So currently I
have a choice of either using version 1.13 (which with
Onedep no longer accepting pdb files makes things a bit
inconvenient as is nice to use the latest version for
getting the mmcif and validation), or to use 1.16, but
switch off the XYZ(real-space). <br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span>Has anyone else
noticed this happening? Found a solution to the problem?</span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span>Thank you for any
suggestions,</span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span>Gyles Cozier.</span><br>
</p>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-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>
</body>
</html>