James must be too fast - he better be to follow the 93,000 (or is it  
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