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
>>>>
>
