[phenixbb] Hydrogen occupancies

[Florian Sauer]

Dear all,

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.
After this refinement the occupancies of some hydrogens dropped to 0 
which makes me a little concerned.

See e.g.:


ATOM    752  H   LYS A  45      -7.443   2.613   9.537  1.00  
4.73           H
ATOM    753  HA  LYS A  45      -9.707   1.128   9.401  0.55  
2.42           H
ATOM    754  HB2 LYS A  45      -8.476   2.797   7.435  1.00 
10.58           H
ATOM    755  HB3 LYS A  45      -9.795   1.948   7.166  0.95  
8.70           H
ATOM    756  HG2 LYS A  45     -10.840   3.210   8.889  0.00 
33.83           H
ATOM    757  HG3 LYS A  45      -9.604   4.206   8.775  0.00 
33.83           H
ATOM    758  HD2 LYS A  45     -11.227   3.615   6.563  0.00 
62.10           H
ATOM    759  HD3 LYS A  45     -11.508   4.867   7.507  0.00 
62.10           H
ATOM    760  HE2 LYS A  45      -9.229   5.527   6.985  1.00 
83.62           H
ATOM    761  HE3 LYS A  45      -9.348   4.488   5.786  0.00 
83.86           H
ATOM    762  HZ1 LYS A  45     -10.909   5.758   4.853  1.00 
99.63           H
ATOM    763  HZ2 LYS A  45     -11.131   6.534   6.042  
0.35100.44           H
ATOM    764  HZ3 LYS A  45      -9.917   6.715   5.257  
0.39100.08           H



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?

Thank you in advance for your answers,

Florian
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