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More thoughts on polarization, divergence, time-stamps in CBF

• To: imgcif-l@bnl.gov
• Subject: More thoughts on polarization, divergence, time-stamps in CBF
• From: Harry Powell <harry@mrc-lmb.cam.ac.uk>
• Date: Fri, 13 Oct 2000 12:09:54 +0100 (BST)

Hi folks

I've been thinking about this problem with the polarization. As David
Brown pointed out, the item

> _diffrn_radiation.polarisation_collimation - this takes an argument
> (modifier?), examples of which are; 
> 
>       pinhole or mirrors with unpolarised beam
>       graphite monochromator
>       synchrotron

is not currently defined in the CIF dictionaries (though it is in the
data harvesting stuff produced by the EBI). However, I'm not at
all sure that collimation and polarization should be combined in one
item anyway.

Also, the item 

	_diffrn_radiation.polarisn_ratio

is used in the EBI stuff and uses the (Ih-Iv)/(Ih+Iv) convention for
the polarization ratio (and which can vary between -1 and +1).  If we
were to define this item, it could only cause confusion with an item
which _is_ defined in core CIF, i.e.

	_diffrn_radiation_polarisn_ratio

which is (essentially) Iv/Ih, and can vary between 0 and infinity. The 
core CIF definition of 

	_diffrn_radiation_polarisn_norm

is the angle in degrees between the perpendicular component and the
diffraction plane, which is based on a four-circle diffractometer with 
a point detector; this is not a useful definition for most people
involved in macromolecular crystallography. For the purpose of
processing diffraction images, it makes good sense to define the plane
explicitly in terms of the incident radiation beam and the raster
direction of the detector with highest precedence (any polarization
correction will be made with reference to the diffraction maximum's
position on the detector).

So, what I'd like to propose is that IUCr scrap its definition of
_diffrn_radiation_polarisn_ratio and use something more sensible,
e.g. the EBI definition, or even Stokes Parameters (which have other
advantages, and I think are very close to what Jim uses).

At the same time, it makes good sense to get the spelling right
(that's polarize with a "Z" not polareese with an "S"...)!

It makes sense to have a more flexible arrangement than the current
IUCr category (which doesn't have sub-items) and instead have
something which _does_ use category items, as much of the imgCIF/CBF
stuff does already.

If we have

 	_diffrn_radiation_polarizn

as a category, then we can have

	_diffrn_radiation_polarizn.ratio
	_diffrn_radiation_polarizn.norm
	_diffrn_radiation_polarizn.stokes_i
	_diffrn_radiation_polarizn.stokes_q
	_diffrn_radiation_polarizn.stokes_u
	_diffrn_radiation_polarizn.stokes_v

--------------------------------------------------------------------------

While I'm thinking about this, it occurred to me that there doesn't
seem to be a token for the divergence of the incident radiation
either. So there should be in the core CIF dictionary items like;

	_diffrn_source_divh
	_diffrn_source_divv
 
Where divh & divv refer to the horizontal and vertical divergences
with respect to the horizontal and vertical (more correct would be to
have them wrt primary and secondary precedence of the) raster
directions of the detector.

--------------------------------------------------------------------------

In my discussions with people about imgCIF/CBF, another item has
arisen; unless I'm missing something, there is no "time-stamp" item
for the image. This is certainly useful information which is included
in many current image formats and which I'd like to see in the
CBF. Something like

	_diffrn_scan.date_start
	_diffrn_scan.date_end

using a standard UNIX style date format would be appropriate.


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

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