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Re: polarization

• To: imgcif-l@bnl.gov
• Subject: Re: polarization
• From: Harry Powell <harry@mrc-lmb.cam.ac.uk>
• Date: Tue, 12 Sep 2000 10:53:10 +0100 (BST)
• In-Reply-To: <Pine.BSF.4.10.10009111038050.18775-100000@epsilon.pair.com>

> On Mon, 11 Sep 2000, Herbert J. Bernstein wrote:

> tag. Perhaps we also need to consider measures of polarization other than
> a ratio.

I couldn't agree more, except to say that it does depend on what the ratio
is you're using. As I understand it, the core CIF ratio is the ratio of
the perpendicularly polarized to the parallel polarized component, which
means there's a range of from 0 - infinity, which strikes me as daft.

The value used for the polarization in common software (and also the
figure used in Giacovazzo's book from a few years back) is the ratio
(Ih-Iv)/(Ih+Iv) {Ih = intensity of the electric vector in the horizontal
plane, Iv ditto in vertical plane}, which could conceivably vary from -1
to +1. Of course, the "horizontal" and "vertical" planes have to be
defined, (IMHO) with respect to a laboratory set of axes.

> On Mon, 11 Sep 2000, Jim Pflugrath wrote:

> I use the polarization that Wolfgang Kabsch defined in his 1988 paper.
> It consists of the degree of polarization and a vector which defines
> a normal to the plane of polarization.  So core CIF almost has it with
> this vector implicit.  The vector is defined is terms of the lab
> coordinate system (remember the MSC system?).
>
> Jim
>

I notice on reading through the HARVESTing code supplied by Kim Henrick of
the EBI that the following items exist and appear to be suitable for our
use here;

_diffrn_radiation.polarisn_ratio - this uses the polarization value
supplied to MOSFLM or Denzo

_diffrn_radiation.polarisation_collimation - this takes an argument
(modifier?), examples of which are; 

	pinhole or mirrors with unpolarised beam
	graphite monochromator
	synchrotron

BTW, my _English_ Oxford English Dictionary spells "polariz-{e,ation}"
with a "z", which also seems to be the American convention ;-)

Harry 
-- 
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH

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