Re: [ccp4bb] into the looking glass

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2008 <-- April 2008 <-- 01 April 2008

Previous message:
Subject: Re: into the looking glass
From: Steve Lane drsteve {- at -} DOUDNA {- dot -} BERKELEY {- dot -} EDU
Date: 2008-04-01

Next message:
Subject: advice regarding computer hardware purchase
From: Chu-Young Kim dbskcy {- at -} GMAIL {- dot -} COM
Date: 2008-04-01

Subject: Re: into the looking glass
From: So Iwata so_iwata {- at -} MAC {- dot -} COM
Date: 2008-04-01

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 navigation

CCP4bb <-- 2008 <-- April 2008 <-- 01 April 2008

Previous message:
Subject: Re: into the looking glass
From: Steve Lane drsteve {- at -} DOUDNA {- dot -} BERKELEY {- dot -} EDU
Date: 2008-04-01

Next message:
Subject: advice regarding computer hardware purchase
From: Chu-Young Kim dbskcy {- at -} GMAIL {- dot -} COM
Date: 2008-04-01