Hi Sara,
- what you observe should not happen since phenix.refine uses riding
model for H atoms. The hydrogen's B-factors are automatically inherited
from the atoms these hydrogens are bonded to. For example, in X-H bond
the B-factor of X should be equal to B-factor of H.
- make sure you are using the latest version of PHENIX:
http://www.phenix-online.org/download/
- if this does not help, please contact me directly, and send the data
and model so I can tell you what exactly is not right (all the files
will be handled confidentially).
- there is PHENIX bulletin board:
http://www.phenix-online.org/mailman/listinfo/phenixbb
Pavel.
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 ;)
