[phenixbb] zero B-factors

Pavel Afonine pafonine at lbl.gov
Mon Nov 25 19:58:06 PST 2013

Yes, the threshold for suspicious isn't very clear if resolution is not 
known. If resolution is known it is less unclear.

B-factor ~0.5-5.0 A**2 is normal for resolutions like 0.5A and better, 
while is clearly suspicious for 2A resolution. etc.

If you plot B vs resolution for all PDB entries there is a nice 
correlation; there is slide showing it here (sorry, can't point page 
number - my internet is too slow at the minute):


On 11/25/13 9:35 AM, Nathaniel Echols wrote:
> On Mon, Nov 25, 2013 at 8:21 AM, Engin Özkan <eozkan at stanford.edu
> <mailto:eozkan at stanford.edu>> wrote:
>     I was looking at this histogram when I wrote that email :) but that
>     histogram is not clickable and does not report residue names (unlike
>     the list just below it). I always look at the histogram (and its
>     usually Poisson-like shape is intriguing). It was just a suggestion
>     to add the other end of the distribution to the list of outlier
>     residues reported by Phenix.
> Good point - I will add this.  The next version of the validation in
> Phenix (phenix.molprobity, not yet available in the GUI) will already
> flag waters with suspiciously low B-factors, although the threshold for
> suspicion is arbitrarily defined right now.
> -Nat
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