[phenixbb] Hydrogen occupancy issue?

[Pavel Afonine]

Hi Mischa,

I just made up an example with fake data and model:
http://cci.lbl.gov/~afonine/for_mischa/

and it seems to work fine using my current development source code. So, 
even if it doesn't work with the most recent version (8-11-2008) 
(although I didn't try, may be it works), it will definitely work in the 
next version.

Cheers,
Pavel.

On 10/17/2008 7:55 AM, Mischa Machius wrote:
> 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?
>
> Example:
> ...
> 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
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>