[phenixbb] Hydrogen occupancy issue?
Pavel Afonine
PAfonine at lbl.gov
Fri Oct 17 10:30:08 PDT 2008
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
>
>
>
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