On Jan 19, 2012, at 10:05 PM, Dale Tronrud wrote: > ... > If someone wrote in their paper "the Rossmann method was used to > solve this structure" what method would come to mind? >
The American method of course! Place the crystal in the beam, allow the autoindexing routine to find the crystal orientation (here the American method stops however), then continue to process the data. Then take a sphere, do MR, and phase extend using NCS and solvent flattening. My previous message, as well as this one, was intended to be a joke (kind of). Sincerely, Petr P.S. Dale, I am sorry you are likely to receive this message twice... > Dale Tronrud > > On 1/19/2012 12:51 PM, 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 >>>>
