<div dir="ltr">Pavel and Nathaniel,<div style> I had the same problem with both phenix-1.8.1-1168 and phenix-1.8.2-1309. The current nightly build (phenix-dev-1334) worked flawlessly. In fact the b-factors make a lot more sense across the whole structure now, typically tripling the mean value and being in better agreement with the statistics for structures of similar resolution. </div>
<div style><br></div><div style>Cheers</div><div style><br></div><div style>Stephen</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 5 April 2013 18:31, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@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 bgcolor="#FFFFFF" text="#000000">
<div>Hi Stephen,<br>
<br>
please use recent Phenix version and the problem will go away:<br>
<br>
<a href="http://www.phenix-online.org/download/nightly_builds.cgi" target="_blank">http://www.phenix-online.org/download/nightly_builds.cgi</a><span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div><div class="h5"><br>
<br>
On 4/5/13 7:44 AM, Stephen Weeks wrote:<br>
</div></div></div>
<blockquote type="cite"><div><div class="h5">
<div dir="ltr">Dear phenixBBers
<div><br>
<div> I have a curious case of refinement of a
2.6 Angs structure, where some of the atoms have a
calculated b-factor of 0.00. It seems to be somewhat random
where this occurs and includes atoms within the backbone
e.g. the nitrogen in the following residue:</div>
<div><br>
</div>
<div>
<div>ATOM 2014 N THR A 264 -2.685 <a href="tel:42.357%20-35.833" value="+14235735833" target="_blank">42.357 -35.833</a>
1.00 0.00 N</div>
<div>ATOM 2015 CA THR A 264 -3.952 <a href="tel:41.776%20-35.425" value="+14177635425" target="_blank">41.776 -35.425</a>
1.00 1.50 C</div>
<div>ATOM 2016 CB THR A 264 -4.684 <a href="tel:41.052%20-36.593" value="+14105236593" target="_blank">41.052 -36.593</a>
1.00 1.70 C</div>
<div>ATOM 2017 OG1 THR A 264 -4.077 39.772 -36.846
1.00 2.24 O</div>
<div>ATOM 2018 CG2 THR A 264 -4.669 <a href="tel:41.867%20-37.855" value="+14186737855" target="_blank">41.867 -37.855</a>
1.00 1.72 C</div>
<div>ATOM 2019 C THR A 264 -3.687 <a href="tel:40.729%20-34.368" value="+14072934368" target="_blank">40.729 -34.368</a>
1.00 2.42 C</div>
<div>ATOM 2020 O THR A 264 -2.571 40.210 -34.263
1.00 2.63 O</div>
<div><br>
</div>
<div>The structure contains 4 NCS related monomers
but with a quick glance I don't see any obvious
correlation between each one as to which atoms are 0.00.
I did use phenix.pdbtools to randomise the B-factors (no
atoms had a value 0.00 afterwards) but upon repeating
the refinement the same problem occurs.</div>
<div><br>
</div>
<div>Does anyone have a suggestion how to fix this
?</div>
<div><br>
</div>
<div>Cheers</div>
<div><br>
</div>
<div>Stephen </div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
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</div></blockquote>
<br>
</div>
</blockquote></div><br></div>