[phenixbb] How should we estimate the "uncertainty" of the occupancy of an atom?

[Tim Gruene]

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Dear Masaki UNNO,

esds (estimated standard deviations) are calculated by full-matrix
least-squares refinement as we carried out in order to estimate the
uncertaintiy of the occupancy values of the ions in potassium
channels. It is described in the Supplemental Material of
http://www.sciencemag.org/content/346/6207/352
SHELXL will also provide you with the correlation coefficient between
the B-values and the occupancy. If you refine the atom in question
anisotropically, the CC drops a little bit.

Wit dynamic memory allocation the only limit to full-matrix
least-squares refinement is the RAM of your computer (and patience as
it may take some time even with only a single refinement cycle). It
has been done a 1A resolution (PDB ID 4KGD).

Best,
Tim

On 02/11/2015 09:36 AM, Masaki UNNO wrote:
> Hello
> 
> 
> 
> We determined the structure of an enzyme-substrate complex. The
> substrate of the enzyme contains some partially occupied atoms. We
> were able to calculate the occupancies of these atoms using
> PHENIX_refine.
> 
> By the way, I would like to know the uncertainties of the
> occupancies of these atoms. How can I estimate the uncertainties?
> For example, the occupancy of an atom was calculated as 0.65; can
> we write it as 0.65 (+/- 0.05) or 0.65 (+/- 0.1)?  I know that it
> is related to B-factor and depends on the resolution (number of
> diffraction data per parameters), but I would like to know how to
> estimate (calculate?) the uncertainty.  Could someone tell me about
> this issue?
> 
> 
> 
> Best regards
> 
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> Masaki UNNO
> 
> Graduate School of Science and Engineering
> 
> Ibaraki University, JAPAN
> 
> 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
> 
> Tel&Fax +81-294-38-5041
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 
> 
> 
> 
> _______________________________________________ phenixbb mailing
> list phenixbb at phenix-online.org 
> http://phenix-online.org/mailman/listinfo/phenixbb
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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