[phenixbb] Hydrogen occupancies

Pavel Afonine pafonine at lbl.gov
Wed Dec 1 11:50:40 PST 2010

  Hi Florian,

> 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 
definitions see:

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!

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