[phenixbb] zero B-factors
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.
> phenixbb mailing list
> phenixbb at phenix-online.org
More information about the phenixbb