Good description from Ian complemented by an amusing aside from Peter.
One small point. Ian says
"The answer is that it turns out that the equation ('Kramer-Kronig
relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion,"
Analogous implies the phenomena are separate. In fact one can derive the
refractive indices from the atomic scattering factors. See for example
http://xdb.lbl.gov/Section1/Sec_1-7.pdf
Particularly equation 1.
Colin
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter
Moody
Sent: 28 January 2012 09:35
To: ccp4bb
Subject: Re: [ccp4bb] MAD
Ian,
If you visit Isaac Newton's old home at Woolsthorpe (near here) you will see a
conflicting claim for location of the classic prism experiment. You will also
find an apple tree in the garden, but that is another story......
Peter
PS this is my special ccp4bb email account, it doesn't always get the attention
it deserves.
On 19 January 2012 17:50, Ian Tickle
<ianj...@gmail.com<mailto:ianj...@gmail.com>> wrote:
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism. This is
of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.
Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it can
be determined by very careful and precise interferometric experiments.
It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned. The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction? The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor, because
the real part of the refractive index is what describes dispersion
(the imaginary part in both cases describes absorption).
So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.
So what does this have to do with the MAD acronym? I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments. At that time Wayne called it multi-wavelength
anomalous dispersion. Tom pointed out that this was really a misnomer
for the reasons I've elucidated above. Wayne liked the MAD acronym
and wanted to keep it so he needed a replacement term starting with D
and diffraction was the obvious choice, and if you look at the
literature from then on Wayne at least consistently called it
multi-wavelength anomalous diffraction.
Cheers
-- Ian
On 18 January 2012 18:23, Phil Jeffrey
<pjeff...@princeton.edu<mailto:pjeff...@princeton.edu>> wrote:
> Can I be dogmatic about this ?
>
> Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
> 254 no. 5028 pp. 51-58
>
> Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
> http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
>
> Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
> (1994). D50, 11-16
>
> etc.
>
>
> I don't see where the problem lies:
>
> a SAD experiment is a single wavelength experiment where you are using the
> anomalous/dispersive signals for phasing
>
> a MAD experiment is a multiple wavelength version of SAD. Hopefully one
> picks an appropriate range of wavelengths for whatever complex case one has.
>
> One can have SAD and MAD datasets that exploit anomalous/dispersive signals
> from multiple difference sources. This after all is one of the things that
> SHARP is particularly good at accommodating.
>
> If you're not using the anomalous/dispersive signals for phasing, you're
> collecting native data. After all C,N,O,S etc all have a small anomalous
> signal at all wavelengths, and metalloproteins usually have even larger
> signals so the mere presence of a theoretical d" difference does not make it
> a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most
> of the time way down in the noise.
>
> Phil Jeffrey
> Princeton
>
>
>
> On 1/18/12 12:48 PM, Francis E Reyes wrote:
>>
>>
>> Using the terms 'MAD' and 'SAD' have always been confusing to me when
>> considering more complex phasing cases. What happens if you have intrinsic
>> Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy
>> atom? Or the MAD+native scenario (SHARP) ?
>>
>> Instead of using MAD/SAD nomenclature I favor explicitly stating whether
>> dispersive/anomalous/isomorphous differences (and what heavy atoms for each
>> ) were used in phasing. Aren't analyzing the differences (independent of
>> source) the important bit anyway?
>>
>>
>> F
>>
>>
>> ---------------------------------------------
>> Francis E. Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
