<div dir="ltr"><div>Dear All,</div><div><br></div>How meaningful are the second derivative based estimates obtained via full matrix inversion when the gradient is not 0 (i.e. when not in the minimum)? I can understand that when you are working with high-resolution data and your R-value is close to 0, things could work, but what happens when around a more challenging 2A? <div><br><div>If you are interested in the uncertainty of the occupancy, I recommend not doing any refinement, but just generate a list of occupancies and B-values for the atom of interest and compute the (free) likelihood for each model. Subsequent normalisation of the neg-exponent of these values, should provide you with an answer that could be just as believable as any other method around. A little bit of python scripting should do the trick quite easily.</div><div><br></div><div>Both the full matrix inversion and the suggestion above probe the steepness of the data-agreement hole the structure is sitting in. Pavels suggestion explores the spread of local minima around the starting configuration. I am not sure what method is more appropriate, perhaps it is instructive to know what problem you are trying to solve.</div><div><br></div><div>HTH</div><div>P</div><div> </div><div><br></div><div><br></div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 11 February 2015 at 16:13, Masaki UNNO <span dir="ltr"><<a href="mailto:unno19@mx.ibaraki.ac.jp" target="_blank">unno19@mx.ibaraki.ac.jp</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all<br>
<br>
Thank you very much for your suggestions.<br>
I will try making a number of models in which the atom has different<br>
occupancies (e.g. 0.1-1.0). Then, I will refine them by restraining the<br>
B-factors.<br>
Actually, our structure contains some reaction intermediates not only the<br>
substrate. So I would like to estimate the ratio.<br>
<br>
Best regards<br>
<span class="HOEnZb"><font color="#888888"><br>
Masaki<br>
</font></span><span class="im HOEnZb">-----Original Message-----<br>
From: <a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a><br>
[mailto:<a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>] On Behalf Of Pavel Afonine<br>
</span><span class="im HOEnZb">Sent: Thursday, February 12, 2015 6:36 AM<br>
To: Dale Tronrud; <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
Subject: Re: [phenixbb] How should we estimate the "uncertainty" of the<br>
occupancy of an atom?<br>
<br>
</span><div class="HOEnZb"><div class="h5">Hi Dale,<br>
<br>
> P.S. I'll look up the paper you reference but my university does not<br>
> subscribe to acta Cryst and getting those papers takes time.<br>
<br>
it is open access:<br>
<br>
<a href="http://phenix-online.org/papers/wd5073_reprint.pdf" target="_blank">http://phenix-online.org/papers/wd5073_reprint.pdf</a><br>
<br>
All the best,<br>
Pavel<br>
<br>
<br>
<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div>-----------------------------------------------------------------<br>P.H. Zwart<br>Staff Scientist<br>Berkeley Center for Structural Biology, Science lead<br>Lawrence Berkeley National Laboratories<br>1 Cyclotron Road, Berkeley, CA-94703, USA<br>Cell: 510 289 9246<br>SASTBX: <a href="http://sastbx.als.lbl.gov" target="_blank">http://sastbx.als.lbl.gov</a></div><div>BCSB: <a href="http://bcsb.als.lbl.gov" target="_blank">http://bcsb.als.lbl.gov</a><br></div><div>PHENIX: <a href="http://www.phenix-online.org" target="_blank">http://www.phenix-online.org</a></div><div>-----------------------------------------------------------------</div></div></div>
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