Hi Sara,
I don't know what "a good average B" is (or what "a bad average B" is).
I know that the <B-iso> for the refined structure should fall in the
same ball-park range than the temperature factor of the data computed
from the Wilson plot. I am not saying that they should match exactly
though. If they really differ wildly (e.g. 10 A**2 vs 140**2) then you
double check things. Like the resolution range used to compute the
Wilson B. And at 1.9-2.0 A resolution you should be able to compute a
proper Wilson B.
Fred
Sara Züger wrote:
Dear CCP4bb,
since the discussion about H-atoms is on, I wanted to ask about what I saw
during my refinements:
I did refinement with phenix of my 1.9-2.0 Angstroem structures and included the hydrogens (riding). However, when I checked on the statistics (refinement close to the end), the average B-factor was extremely high (in phenix.polygon it was higher than with any other structure in similar resolution range). It makes sense though that this happens, if you have a residue which has a high B-factor and carries a lot of hydrogens the average B-factor will raise quite a lot (since the B-factor of hydrogens is calculated 1-1.5x of B-factor from the atom it sits on), right?
(When I removed the hydrogens again, the average B-factor was fine...)
My question is now did I do something wrong in my refinement (-> do I have to
change something that this does not happen), or is this something everybody sees?
If this is common, what would happen (during evaluation) if you want to publish
a structure and the statistics show such a high average B-factor? Is it better
to have hydrogens on, but a bad average B, or no hydrogens on and a good
average B... Obviously, I never published a structure ;)
Thanks for sharing your opinion!
Sara
