Re: [ccp4bb] into the looking glass

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: into the looking glass
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2008-04-01

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Subject: Re: into the looking glass
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-04-01

Subject: Re: into the looking glass
From: anthony {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU anthony {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-04-01

Have to learn crystallography again.............. and now along with
quantum mechanics!

worried....

Anthony

> 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
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: into the looking glass
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2008-04-01

Next message:
Subject: Re: into the looking glass
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-04-01