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Re: [ccp4bb] into the looking glass |
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CCP4bb navigationCCP4bb <-- 2008 <-- April 2008 <-- 01 April 2008Subject: Re: into the looking glass From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL Date: 2008-04-01 more?) csh lines of code in Elves in the speed I recall he does. So, most likely he lost less time writing it than us reading it: its a cunning plot, he is wasting our time not his. A. On 1 Apr 2008, at 21:54, So Iwata wrote: > Great job. But don't you have any better things to do (tm) ? s. > > On 1 Apr 2008, at 18:59, James Holton wrote: >> >> Dear CCP4BB, >> >> I think it prudent at this point for me to announce what could >> be a very old, but serious error in the fundamental mathematics of >> crystallography. To be brief, I have uncovered evidence that the >> "hand" of the micro-world is actually the opposite of what we have >> believed since Bijvoet's classic paper in 1951. >> >> Those of you who know me know that I have been trying to lay >> down the whole of x-ray diffraction into a single program. This >> is harder than it sounds. We all know what anomalous scattering >> is, but a detailed description of the math behind translating this >> "dynamical theory" effect all the way to the intensity of a >> particular detector pixel is hard to find all in one place. Most >> references in the literature about how anomalous scattering is >> connected to absolute configuration point to the classic Nature >> paper: Bijvoet et. al. (1951). Unfortunately, since this is a >> Nature paper, it is too short to describe the math in detail. For >> the calculations, the reader is referred to another paper by >> Bijvoet in the Proc. Roy. Acad. Amsterdam v52, 313 (1949). >> Essentially, the only new information in Bijvoet et. al. (1951) is >> the assertion that Emil Fischer "got it right" in his initial >> (arbitrary) assignment of the "R" and "S" reference compounds for >> the absolute configuration of molecules. >> I decided to follow this paper trail. The PRAA document was >> hard to come by and, to my disappointment, again referenced the >> "real" calculation to another work. Eventually, however, all >> roads lead back to R. W. James (1946). This is the definitive >> textbook on scattering theory (originally edited by Sir Lawrence >> Bragg himself). It is extremely useful, and I highly recommend >> that anyone who wants to really understand scattering should read >> it. However, even this wonderful text does not go through the >> full quantum-mechanical derivation of scattering, but rather rests >> on J. J. Thompson's original classical treatment. There is >> nothing wrong with this because the the exact value of the phase >> lag of the scattering event does not effect anything as long as >> the phase lag from all the atoms is the same. The only time it >> does become important is anomalous scattering. Even so, changing >> the sign of the phase lag will have no effect on any of the >> anomalous scattering equations as long as all the anomalous >> contributions have the same sign. The only time the sign of the >> phase lag is important is in the assignment of absolute >> configuration. Unfortunately, a full quantum mechanical treatment >> of the scattering process DOES produce a phase lag with the >> opposite sign of the classical treatment. This is not the only >> example of this sort of thing cropping up. One you can find in >> any quantum text book is the treatment of "tilting" a quantum- >> mechanical spin (such as an electron). It was shown by Heisenberg >> that a "tilt" of 360 degrees actually only turns an electron >> upside-down. You have to "tilt" it by 720 degrees to restore the >> initial state, or get it "right-side-up" again. This is very >> counterintuitive, but true, and unfortunately a similar treatment >> of scattering results in a phase lag of +270 degrees to "restore" >> the electron after the scattering event, not +90 degrees as was >> derived classically. To be brief, there is a sign error. >> >> Perhaps the reason why noone caught this until now is not just >> that the quantum calculations are a pain, but that it was very >> tempting to accept that the large body of literature following >> Fischer's convention would not have to be "corrected" by inverting >> the hand of every chiral center described up to that time. >> Unfortunately, we now have an even larger body of literature >> (including the PDB) that must now be "corrected". >> >> It is an under-appreciated fact in chemistry that anomalous >> scattering is arguably the only direct evidence we have about the >> "hand" of the micro-world. There are other lines of evidence, >> such as the morphology of macroscopic crystals and some recent >> STEM-type microscope observations of DNA. However, as someone >> with a lot of experience in motor control I don't mind telling you >> how easy it is to make a sign error in the direction of an axis. >> This is especially easy when the range of motion of the axis is >> too small to see by eye. You end up just swapping wires and >> flipping bits in the axis definitions until you "get it right". >> The "right" configuration (we have all assumed) is the one >> asserted in Bijvoet et. al. (1951). Apparently, the STEM >> observations fell prey to such a "mistake". But can you blame >> them? Inverting the "hand of the world" is going to be very hard >> for a lot of people to accept. Indeed, if anyone can find an >> error in my math, please tell me! I would really like to be wrong >> about this. >> >> -James Holton >> MAD Scientist CCP4bb navigationCCP4bb <-- 2008 <-- April 2008 <-- 01 April 2008 |
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