On Wed, Apr 17, 2013 at 12:41 PM, Brennan Bonnet
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.
Well, there is natural variability in the B-factors at any resolution, and no direct equivalence to the Wilson B-factor calculated from intensity statistics. But the behavior you are seeing is an implementation detail of some versions of Phenix - it all depends on whether the overall scale is incorporated into the atomic B-factors. Because most refinement programs (including most versions of Phenix aside from a few of the 1.8 series) always do this, most crystallographers have come to expect a specific range for B-factors at any given resolution. If you want to be absolutely certain that your committee is happy, just re-run the last round of refinements with the nightly build version - no need to do any re-processing or anything fancy. -Nat