For those of you interested, the reply to Tassos' question can be found
here:
http://www.iucr.org/resources/commissions/crystallographic-computing/schools/school96/ccp4-program-system
(on-line)
as well as here, http://www.*ccp4*.ac.uk/manual.ps (a ps file).
McLaughlin, Terry and Zelinka. And yes, I'm over 40 ! I have also dealt
with LCF files...
Fred.
Anastassis Perrakis 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
