[Ifeffit] Debye Waller factors for Water Molecules

[Paul Fons]

   Thanks everyone (Shelly, Matt, and Anatoly) for the info.   I  
thought it would be fun to learn while trying to work out a  
(relatively) simple system.  I have EXAFS data about a Zn site.  The  
Zn is bonded to three cystedines so I have the DW pretty much under  
control, but for the water molecules.  I will investigate the  
approaches mentioned here and see which one the data is most  
consistent with (I did have the foresight to choose a system for  
which I have high resolution x-ray crystallography data).

			Thanks

					Paul

On Jul 29, 2007, at 12:57 AM, Matt Newville wrote:

> Hi Paul,
>
> A. Vogel et al (Biochemistry 43, p10379, 2004) report a Zn water (or
> OH) at 2.0Ang with sigma2=0.007Ang^2 for data collected at 30K.
>
> This is for a binuclear Zn compound, and the OH is a bridging ligand
> (with the other ligands being dominated by histidine-like rings), so I
> don't know how close it is to your structure.  But it might be a good
> place to start.
>
> Also, the results came from EXCURVE.  That's not to suggest that the
> results are not reliable, but you might want to check carefully the
> meaning of sigma2.  I'm not 100% sure of this (or what the Vogel et al
> paper is reporting), but I think the EXCURVE sigma2 might be a factor
> of 2 bigger than the Ifeffit sigma2.
>
> I'd be a little wary of using an Einstein model for "water"  ligands
> down to 30K.  It would be interesting to hear how well an Einstein
> model compares to the DFT modeling for any ligands in a bio-molecule.
>
> --Matt
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20070730/4cbea1df/attachment.htm>