[phenixbb] Hydrogen occupancy issue?

Mischa Machius Mischa.Machius at utsouthwestern.edu
Fri Oct 17 07:55:38 PDT 2008

Hi - I have a problem regarding occupancies of hydrogens in residues  
with alternate conformations. Specifically, when a residue exists in  
alternate conformations, the H hydrogen of the following residue (the  
one attached to the N) also exists in the same number of alternate  
locations. The occupancies of these hydrogens do not add up to 1.00  
like the occupancies of the hydrogens for the preceding residue do. In  
fact, these occupancies are all 1.00.

Is that a bug, a feature, or did I commit a user error somehow?

ATOM    956  H  AHIS A 293       6.967 -36.722   8.227  1.00  
15.31           H
ATOM    957  H  BHIS A 293       6.913 -36.667   8.216  1.00  
15.31           H
ATOM    958  H  CHIS A 293       6.888 -36.648   8.202  1.00  
15.31           H

The preceding Ser A 292 exists in three alternate conformations with  
occupancies A=0.53, B=0.18, C=0.29; sum = 1.00
The corresponding hydrogens have occupancies A=0.52, B=0.19, C=0.29;  
sum = 1.00 (I can accept that they have somewhat different occupancies  
than the attached heavy atoms, based on a previous thread about this  
issue, although the discrepancies are now much smaller in the 1.3- 
final version compared to 1.3-rc2)
The H hydrogens of the following residue (His A 293) have occupancies  
A=1.00, B=1.00, C=1.00; sum = 3.00, and the RCSB starts yelling.

Should I just manually edit the values and set them to the occupancies  
of the hydrogens in the preceding residue?

Any help appreciated. Thanks so much. Best - MM

Mischa Machius, PhD
Associate Professor
Department of Biochemistry
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353

More information about the phenixbb mailing list