From: James Holton
Date: 19 January 2012 16:34
As a self-declared "MAD Scientist" I suppose I should chime in.
The acronym "MAD" has indeed appeared by several different names in the literature. Here is the "Google vote":
"multiwavelength anomalous diffraction" - 16500 articles in Google Scholar (including Yang et. al. (1990))
"multiwavelength anomalous dispersion" - 6890 articles
"multiple anomalous dispersion" - 3250 articles
"multiple anomalous diffraction" - 956 articles
"multiple anomalous difference" - 3 articles
Clearly, there are thousands of publications that have gotten this "wrong", but which thousands is uncertain. I fully understand that Google Scholar is not the final authority on ... anything, and popular vote is not always the best way to settle scientific naming conventions either. For example, I am still calling Pluto a planet. I am also never going to call San Francisco's Candlestick Park by any of its new names (3COM Park, Monster Park, and now back to Candlestick!). And the "Artist Formerly Known as Prince" was always "Prince" to me. The reason for my personal inertia about name changes is that I need to hear a scientifically compelling reason for them. Why do I care? Because the scientific literature is supposed to be archival, and as a scholar who often finds himself going through this archive trying to find the original reference for various things, I find "nomenclature drift" endlessly infuriating.
Then again, the name given by the originating author is not always the best name either. Nobody calls Patterson maps an "F-square synthesis" (as Patterson did).
Oh, and although many lemmings do drown in big rivers and even the ocean, their legendary periodic mass suicide runs have been greatly exaggerated. A few years back, the Disney film crew who made the "White Wilderness" documentary admitted that the little guys did need some "encouragement" for the really good shots they wanted.
So, it would appear that even lemmings have some sense in their tiny little heads? Do we? Does anyone have a scientifically compelling reason to call MAD something other than "multiwavelength anomalous diffraction"?
-James Holton
MAD Scientist
On Wed, Jan 18, 2012 at 12:28 PM, Ethan Merritt wrote:
----------
From: Ian Tickle
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
> 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
----------
From: Mark J van Raaij
So, with the combined votes of Hendrickson, Blundell, Tickle and Google, can we safely call it "Multi-wavelength Anomalous Diffraction" from now on and call all other names wrong?
Mark
----------
From: Marcus Winter
... or just call it 'MAD', and you're bound to be correct !!
Everything is in the eye of the beholder, after all.
Marcus.
----------
From: Ethan Merritt
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
----------
From: Petr Leiman
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
----------
From: Anastassis Perrakis
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.
----------
From: Dale Tronrud
How many names do you propose to use to describe SIRAS?
If someone wrote in their paper "the Rossmann method was used to
solve this structure" what method would come to mind?
Dale Tronrud
----------
From: Petr Leiman
On Jan 19, 2012, at 10:05 PM, Dale Tronrud wrote:
> ...
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...
----------
From: Lawrence Shapiro
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)?
----------
From: Gerard Bricogne
Dear Petr and other contributors to this thread,
I think it is never easy to call a method by that of "its inventor", as
there are usually many more than one inventor of the total know-how that
gets incorporated into the finished product that people end up using. Names
such as those of James Phillips, Roger Fourme and Richard Kahn, spring to
mind when it comes to the early histories of the MAD and SAD methods.
In my opinion, thought and effort would be much better spent revisiting
these methods from the point of view of applying them better (e.g by
providing better protocols on beamlines to optimise the signal-to-noise
ratio of anomalous and dispersive differences) rather than deconstructing
acronyms and launching popularity contests for putative single inventors.
The latter is a profound misunderstanding of how methods appear and are
developed, and this kind of personality cult is best left to cheap TV
entertainment :-) - a baseline above which this BB surely wishes to remain.
With best wishes,
Gerard.
--
--
----------
From: <mjvdwoerd
----------
From: Vellieux Frederic
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.
----------
From: Jrh
Dear Colleagues,
The real issue is the 'anomalous' word introduced as an X-ray scattering theory correction, which was not anomalous but the actual physical situation of resonance scattering. Thus the most recent of the Anomalous Scattering conferences was correctly called REXS2011. Ie Resonant Elastic X-ray Scattering.
The 1975 Anomalous Scattering Conference book incidentally has the Hoppe and Jakubowski Ni and Co K alpha two wavelength study either side of the Fe K edge for phase determination of the erythrocruorin protein, in turn based on the Okaya and Pepinsky 1956 formalism. These are MAD but 'simply' not synchrotron.
Francis Crick's autobiography 'What Mad Pursuit' will give you a further link to MAD, based on weak ie small intensity changes.
Just to also mention I regularly refer to the 'Hendrickson Se-met MAD' method.
The history is interesting. Keith Hodgson is a must mention name, as is Stanford Synchrotron Radiation Laboratory.
A most recent wrinkle in nomenclature in this area is the use in chemical crystallography by some of Resonant scattering for off resonance ie in determining the hand of organics. At present I see no way around correcting such mentions but with the unfortunate term:-
Off-resonance resonance scattering Flack parameter determination of the hand.
Greetings,
John
Prof John R Helliwell DSc
----------
From: Peter Moody
Ian,
----------
From: Colin Nave
Good description from Ian complemented by an amusing aside from Peter.
One small point. Ian says
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
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.
----------
From: Ian Tickle
Hi Peter
You are right: the location of the prism experiment is most likely the
study at Woolsthorpe, e.g. see
http://www.isaacnewton.org.uk/texts/OfColours7 . Newton was admitted
to Trinity College in 1661 as a 'sizar' (a paid part-time student
employed by the College) but was forced to return to Woolsthorpe (the
family home) in August 1665 (http://www.isaacnewton.org.uk/Chronology)
to continue studying privately, because the University closed
temporarily as a precaution against the Great Plague ('Black Death')
which was spreading outwards from the initial outbreak in this country
in the London Docklands during the summer of that year. He returned
to Trinity in 1667 as a Fellow of the College.
So I should have been more precise and said that Newton performed the
prism experiment during the time that he was associated with Trinity
(it's not clear what the nature of his association with Trinity was
during the 2 years he spent doing experiments at Woolsthorpe).
Cheers
-- Ian
----------
From: Bernhard Rupp (Hofkristallrat a.D.)
For the history buffs and crystallographers needing some R&R and chill-out,
an interesting historic fiction read about the era of Newton and Leibnitz
and the foundation of the Royal Society is the Baroque cycle by Neil
Stevenson.
http://en.wikipedia.org/wiki/The_Baroque_Cycle
Cryptonomicon, although written before, picks up a descendent of a character
from the Cycle, and can be considered imho the 4th book
http://en.wikipedia.org/wiki/Cryptonomicon
All together ~ 2400 pages. Cheap on Amazon 3rd party. Book a long vacation.
Best, BR
Date: 19 January 2012 16:34
As a self-declared "MAD Scientist" I suppose I should chime in.
The acronym "MAD" has indeed appeared by several different names in the literature. Here is the "Google vote":
"multiwavelength anomalous diffraction" - 16500 articles in Google Scholar (including Yang et. al. (1990))
"multiwavelength anomalous dispersion" - 6890 articles
"multiple anomalous dispersion" - 3250 articles
"multiple anomalous diffraction" - 956 articles
"multiple anomalous difference" - 3 articles
Clearly, there are thousands of publications that have gotten this "wrong", but which thousands is uncertain. I fully understand that Google Scholar is not the final authority on ... anything, and popular vote is not always the best way to settle scientific naming conventions either. For example, I am still calling Pluto a planet. I am also never going to call San Francisco's Candlestick Park by any of its new names (3COM Park, Monster Park, and now back to Candlestick!). And the "Artist Formerly Known as Prince" was always "Prince" to me. The reason for my personal inertia about name changes is that I need to hear a scientifically compelling reason for them. Why do I care? Because the scientific literature is supposed to be archival, and as a scholar who often finds himself going through this archive trying to find the original reference for various things, I find "nomenclature drift" endlessly infuriating.
Then again, the name given by the originating author is not always the best name either. Nobody calls Patterson maps an "F-square synthesis" (as Patterson did).
Oh, and although many lemmings do drown in big rivers and even the ocean, their legendary periodic mass suicide runs have been greatly exaggerated. A few years back, the Disney film crew who made the "White Wilderness" documentary admitted that the little guys did need some "encouragement" for the really good shots they wanted.
So, it would appear that even lemmings have some sense in their tiny little heads? Do we? Does anyone have a scientifically compelling reason to call MAD something other than "multiwavelength anomalous diffraction"?
-James Holton
MAD Scientist
On Wed, Jan 18, 2012 at 12:28 PM, Ethan Merritt wrote:
On Wednesday, 18 January 2012, Soisson, Stephen M wrote:
But if we were to follow that convention we would have been stuck with Multi-wavelength Resonant Diffraction Experimental Results, or, quite simply, MuRDER.
You could switch that to Multiple Energy Resonant Diffraction Experiment
but I don't think that would help any.
As to "anomalous" - the term comes from the behaviour of the derivative
delta_(optical index) / delta_(wavelength)
This term is positive nearly everywhere, but is anomalously negative
at the absorption edge.
Ethan
-----Original Message-----
From: CCP4 bulletin board On Behalf Of Jacob Keller
Sent: Wednesday, January 18, 2012 3:13 PM
Subject: Re: [ccp4bb] Merging data collected at two different wavelength
This begs the question* whether you want the lemmings to understand
you. One theory of language, gotten more or less from Strunk and
White's Elements of Style, is that the most important feature of
language is its transparency to the underlying thoughts. Bad language
breaks the transparency, reminds you that you are reading and not
simply thinking the thoughts of the author, who should also usually be
invisible. Bad writing calls attention to itself and to the author,
whereas good writing guides the thoughts of the reader unnoticeably.
For Strunk and White, it seems that all rules of writing follow this
principle, and it seems to be the right way to think about language.
So, conventions, even when somewhat inaccurate, are important in that
they are often more transparent, and the reader does not get stuck on
them.
Anyway, a case in point of lemmings is that once Wayne Hendrickson
himself suggested that the term anomalous be decommissioned in favor
of "resonant." I don't hear any non-lemmings jumping on that
bandwagon...
JPK
*Is this the right use of "beg the question?"
On Wed, Jan 18, 2012 at 1:57 PM, Phoebe Rice wrote:
>>
>>> Can I be dogmatic about this ?
>>
>>I wish you could, but I don't think so, because even though those
>>sources call it that, others don't. I agree with your thinking, but
>>usage is usage.
>
> And 10,000 lemmings can't be wrong?
----------
From: Ian Tickle
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
> 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
----------
From: Mark J van Raaij
So, with the combined votes of Hendrickson, Blundell, Tickle and Google, can we safely call it "Multi-wavelength Anomalous Diffraction" from now on and call all other names wrong?
Mark
----------
From: Marcus Winter
... or just call it 'MAD', and you're bound to be correct !!
Everything is in the eye of the beholder, after all.
Marcus.
----------
From: Ethan Merritt
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
----------
From: Petr Leiman
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
----------
From: Anastassis Perrakis
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.
----------
From: Dale Tronrud
How many names do you propose to use to describe SIRAS?
If someone wrote in their paper "the Rossmann method was used to
solve this structure" what method would come to mind?
Dale Tronrud
----------
From: Petr Leiman
On Jan 19, 2012, at 10:05 PM, Dale Tronrud wrote:
> ...
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...
----------
From: Lawrence Shapiro
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)?
----------
From: Gerard Bricogne
Dear Petr and other contributors to this thread,
I think it is never easy to call a method by that of "its inventor", as
there are usually many more than one inventor of the total know-how that
gets incorporated into the finished product that people end up using. Names
such as those of James Phillips, Roger Fourme and Richard Kahn, spring to
mind when it comes to the early histories of the MAD and SAD methods.
In my opinion, thought and effort would be much better spent revisiting
these methods from the point of view of applying them better (e.g by
providing better protocols on beamlines to optimise the signal-to-noise
ratio of anomalous and dispersive differences) rather than deconstructing
acronyms and launching popularity contests for putative single inventors.
The latter is a profound misunderstanding of how methods appear and are
developed, and this kind of personality cult is best left to cheap TV
entertainment :-) - a baseline above which this BB surely wishes to remain.
With best wishes,
Gerard.
--
----------
From: <mjvdwoerd
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
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
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From: Vellieux Frederic
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.
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From: Jrh
Dear Colleagues,
The real issue is the 'anomalous' word introduced as an X-ray scattering theory correction, which was not anomalous but the actual physical situation of resonance scattering. Thus the most recent of the Anomalous Scattering conferences was correctly called REXS2011. Ie Resonant Elastic X-ray Scattering.
The 1975 Anomalous Scattering Conference book incidentally has the Hoppe and Jakubowski Ni and Co K alpha two wavelength study either side of the Fe K edge for phase determination of the erythrocruorin protein, in turn based on the Okaya and Pepinsky 1956 formalism. These are MAD but 'simply' not synchrotron.
Francis Crick's autobiography 'What Mad Pursuit' will give you a further link to MAD, based on weak ie small intensity changes.
Just to also mention I regularly refer to the 'Hendrickson Se-met MAD' method.
The history is interesting. Keith Hodgson is a must mention name, as is Stanford Synchrotron Radiation Laboratory.
A most recent wrinkle in nomenclature in this area is the use in chemical crystallography by some of Resonant scattering for off resonance ie in determining the hand of organics. At present I see no way around correcting such mentions but with the unfortunate term:-
Off-resonance resonance scattering Flack parameter determination of the hand.
Greetings,
John
Prof John R Helliwell DSc
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From: Peter Moody
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.
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From: Colin Nave
Good description from Ian complemented by an amusing aside from Peter.
One small point. Ian says
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
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.
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From: Ian Tickle
Hi Peter
You are right: the location of the prism experiment is most likely the
study at Woolsthorpe, e.g. see
http://www.isaacnewton.org.uk/texts/OfColours7 . Newton was admitted
to Trinity College in 1661 as a 'sizar' (a paid part-time student
employed by the College) but was forced to return to Woolsthorpe (the
family home) in August 1665 (http://www.isaacnewton.org.uk/Chronology)
to continue studying privately, because the University closed
temporarily as a precaution against the Great Plague ('Black Death')
which was spreading outwards from the initial outbreak in this country
in the London Docklands during the summer of that year. He returned
to Trinity in 1667 as a Fellow of the College.
So I should have been more precise and said that Newton performed the
prism experiment during the time that he was associated with Trinity
(it's not clear what the nature of his association with Trinity was
during the 2 years he spent doing experiments at Woolsthorpe).
Cheers
-- Ian
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From: Bernhard Rupp (Hofkristallrat a.D.)
For the history buffs and crystallographers needing some R&R and chill-out,
an interesting historic fiction read about the era of Newton and Leibnitz
and the foundation of the Royal Society is the Baroque cycle by Neil
Stevenson.
http://en.wikipedia.org/wiki/The_Baroque_Cycle
Cryptonomicon, although written before, picks up a descendent of a character
from the Cycle, and can be considered imho the 4th book
http://en.wikipedia.org/wiki/Cryptonomicon
All together ~ 2400 pages. Cheap on Amazon 3rd party. Book a long vacation.
Best, BR
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