Re: [phenixbb] zero B-factors

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): http://phenix-online.org/presentations/latest/pavel_validation.pdf Pavel On 11/25/13 9:35 AM, Nathaniel Echols wrote:

On Mon, Nov 25, 2013 at 8:21 AM, Engin Özkan mailto:[email protected]> 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb