<div dir="ltr">It would be nice if the validation procedures looked for B-factor outliers that were too low as well as too high. A very low B-factor can be indicative of the wrong atom, e.g. a water molecule that is actually an ion.<div>
<br></div><div style>Morten</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 18 November 2013 21:38, 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">If you see this problem using the latest Phenix version then please send me files (off-list) necessary to reproduce it and I will investigate.<br>
<br>
If interested what was the "problem" causing zero B-factors please see below.<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<br>
In a nutshell the problem is this. Assuming total model structure factor is (for simplicity):<br>
<br>
F ~ exp(-Boverall_scale * s**2) * exp(-Batoms * s**2)<br>
<br>
it's clear that any combination of Boverall_scale and Batoms that maintains Boverall_scale+Batoms=const will not change total model structure factors (and therefore R-factors, maps, etc).<br>
<br>
The new bulk-solvent and overall scaling algorithm that we implemented sometime in April 2012 and that went into 1.8_1069 originally did not care about returning isotropic component of Boverall_scale back to atoms (Batoms):<br>
<br>
<a href="http://journals.iucr.org/d/issues/2013/04/00/dz5273/dz5273.pdf" target="_blank">http://journals.iucr.org/d/<u></u>issues/2013/04/00/dz5273/<u></u>dz5273.pdf</a><br>
<br>
In fact, it assumed that overall contribution (overall B that is equal for all atoms) should stay in Boverall_scale (indeed, why keep common B in all individual atomic B-factors!?), and the rest goes into Batoms.<br>
This behavior typically generates user concerns about "too small" B-factors.<br>
<br>
An alternative agreement is to postulate that the matrix Boverall_scale is traceless meaning that overall B-factor goes into individual atomic B-factors.<br>
This behavior occasionally generates user concerns about "too large" B-factors.<br>
<br>
A few months later (sometime in end summer/fall 2012) we changed scaling behavior such that overall B-factor stays in individual atomic B-factors.<br>
<br>
All in all, either way is correct and a matter of agreement and preferences, but definitely not a bug.<div class="HOEnZb"><div class="h5"><br>
<br>
<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Morten K Gr�ftehauge, PhD�<div>Pohl Group</div><div>Durham University</div>
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