With the starting remark that Wayne is "larger than life" in my mind, we could
call SAD the "Teeter Method"? I think it has a very nice ring to it and perhaps
Wayne would approve.
I learned something new today. Until now I thought that of course it is called
"dispersion". That is because in the late 1980s I started studying MAD and used
it as topic for my PhD qualifier (which was not allowed to be the same topic as
one's dissertation). So I read every paper I could get my hands on (this was
before internet and electronic access to journals, yes it once was that way,
hard to believe these days). I worried a lot at the time about how it works
exactly, not what it is (was) called. It is probably the case that
crystallography itself isn't intuitive for someone who has never done it and to
add MAD (or SAD) to it...
I shall try to practice "diffraction" from now on. It seems scientifically
preferable.
Mark
-----Original Message-----
From: Lawrence Shapiro <l...@columbia.edu>
To: CCP4BB <CCP4BB@JISCMAIL.AC.UK>
Sent: Thu, Jan 19, 2012 2:48 pm
Subject: Re: [ccp4bb] MAD
I never weigh in, so I don't know if I'll get in trouble here...
How would we distinguish MAD (to now be called "The Hendrickson
Method") from SAD ("The Hendrickson Method" - remeber crambin?
Nature, 1981)?
On Thu, Jan 19, 2012 at 3:59 PM, Anastassis Perrakis <a.perra...@nki.nl> wrote:
> A, yes, inventor's names. Anyone reading who is less than 40 and knows what
MTZ stands for?
>
> ;-)
>
> My favorite technique remains SADDAM - a side product of Gerard's War On
Error, that never did catch-up with the masses - experimentally or as an
acronym.
>
> A.
>
> On 19 Jan 2012, at 21:51, Petr Leiman wrote:
>
>> It would be so much more convenient to call these techniques (MAD, SAD,
>> etc.)
by their inventor's name. This would simplify things immensely simultaneously
eliminating CCP4BB MADisagreements.
>>
>> Although in our days of copyrights wars, the journals and perhaps
>> conferences
where these methods were presented for the first time would insist on using
their names as part of the method's name...
>>
>> Petr
>>
>>
>> On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote:
>>
>>> On Thursday, 19 January 2012, Ian Tickle wrote:
>>>> 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.
>>>
>>> Ian:
>>>
>>> The change-over from "dispersion" to "diffraction" in MAD protein
>>> crystallography happened a couple of years earlier, at least with regard
>>> to work being done at SSRL. I think the last paper using the term
>>> "dispersion" was the 1988 Lamprey hemoglobin paper. The next two papers,
>>> one a collaboration with Wayne's group and the other a collaboration
>>> with Hans Freeman's group, used the term "diffraction".
>>>
>>> WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt.
>>> Crystallographic structure-analysis of lamprey hemoglobin from
>>> anomalous dispersion of synchrotron radiation.
>>> PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988.
>>>
>>> JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata,
>>> KO Hodgson, HC Freeman.
>>> Phase determination by multiple-wavelength X-ray-diffraction -
>>> crystal-structure of a basic blue copper protein from cucumbers.
>>> SCIENCE, 241(4867):806–811, AUG 12 1988.
>>>
>>> WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley.
>>> Crystal structure of core streptavidin determined from multiwavelength
>>> anomalous diffraction of synchrotron radiation.
>>> PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
>>> AMERICA, 86(7):2190–2194, APR 1989.
>>>
>>> On the other hand, David and Lilo Templeton continued to use the term
>>> "anomalous dispersion" for at least another decade, describing their
>>> diffraction experiments exploring polarization effects and other
>>> characteristics of near-edge X-ray scattering by elements all over the
>>> periodic table.
>>>
>>> Ethan
>>>
>>>
>>>> Cheers
>>>>
>>>> -- Ian
>>>>
>>>> On 18 January 2012 18:23, Phil Jeffrey <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
>>>>
>
