[phenixbb] Hydrogen occupancies
pafonine at lbl.gov
Wed Dec 1 11:50:40 PST 2010
> I'm currently refining a small protein against 0.96A data using
> phenix.refine (1.6-486) from the GUI.
> Refinement without hydrogens yielded Rwork/free of 12.4/14.2. I then
> added H-atoms with phenix.reduce and switched to individual refinement
> of hydrogens which dropped the R-factors to 11.3/13.4.
- the drop in r-factors is expected. For review see:
Acta Cryst. (2010). D66, 1153-1163
Joint X-ray and neutron refinement with phenix.refine
P. V. Afonine, M. Mustyakimov, R. W. Grosse-Kunstleve, N. W. Moriarty,
P. Langan and P. D. Adams
- it's always a good idea to use H atoms in refinement, especially at
this high resolution, and a must at ultra-high resolution. For
Acta Cryst. (2009). D65, 1283-1291
On the use of logarithmic scales for analysis of diffraction data
A. Urzhumtsev, P. V. Afonine and P. D. Adams
> After this refinement the occupancies of some hydrogens dropped to 0
> which makes me a little concerned.
I recall even for Aldose Reductase refined at 0.66A resolution we could
see only ~70-80% of all possible H atoms. The are (many) reasons for
this. At 0.96A I would expect to see much less. So this is why
individually refined occupancy of an H atoms may drop to 0.0.
> I would like to ask whether it is possible in phenix to group the
> occupancies to keep them at the same value as the rest of the residue
> but still refine xyz and isotropic adp of the individual hydrogens?
It used to be possible in the past but I removed that functionality (and
now thinking of restoring it back but for a different purpose -:) ). For
now I would just stick to riding model as it seems to be more
appropriate in this case.
All the best!
More information about the phenixbb