[phenixbb] Unusually low B factors

Brennan Bonnet Brennan.Bonnet at lightsource.ca
Wed Apr 17 12:41:16 PDT 2013

Hi Nat,

I'm running version 1.8.2-1309.

I could try this again if I need the newer version.  I'm currently completing my thesis and have processed and reprocessed this data so many times that.  At this point it's getting more important that I wrap up my degree than getting this processing to work 100%.  

I'm hoping that someone else has had this problem with B values before and could offer an explanation like "It's due to gas pressure, or sometimes B values are just low and that's acceptable".  That way I can include it in my thesis so that I don't get grilled by my committee.


From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] On Behalf Of Nathaniel Echols [nechols at lbl.gov]
Sent: Wednesday, April 17, 2013 1:23 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Unusually low B factors

On Wed, Apr 17, 2013 at 12:19 PM, Brennan Bonnet
<Brennan.Bonnet at lightsource.ca> wrote:
> I have produced xenon derivatives for SAD phasing of several standard proteins by placing them under xenon gas pressure and then immediately flash freezing in liquid nitrogen.  Everything has worked out nicely as far as successful phasing, nice models, and low R factors.
> Now I've noticed that the B values have decreased from initial processing values.  Several rounds of manual changes and phenix.refine have caused B values to decrease each round of refinement to values of around 10 (I guess 20 is a more common value).  Does anyone know why this is happening or what the explanation might be?

Which version are you using?  If it's 1.8.2 or earlier, could you
please update to the latest nightly build and try again?

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