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CCP4BB  August 2007

CCP4BB August 2007

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Subject:

Re: Questions about diffraction

From:

Jacob Keller <[log in to unmask]>

Reply-To:

Jacob Keller <[log in to unmask]>

Date:

Fri, 24 Aug 2007 16:15:36 -0500

Content-Type:

text/plain

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Parts/Attachments

text/plain (50 lines)

>For the total integrated energy to be conserved, energy will have to be
>created in certain directions to compensate for the loss in other
>directions. So in a direction in which the condition is met, the total
>will have to be more than the sum of the waves in that direction.

>How about considering the possibility that all photons coming into the
>sample are diffracted -- just in different directions. So that what is
>happening is not constructive and destructive interference but a kind
>sorting of the photons based on a certain property of the photons, maybe
>the phase.

*****

I think of it that each photon that happens to be perturb an electron, i.e., Thomson scattering,
sends out a spherical wave, which has anisotropy to it, i.e., the wave front is more concentrated
in the forward direction. These spherical waves interfere with each other, making the diffraction
pattern.

Something for you to chew on: how is it that the electrons of the protein, which are presumably not 
in phase with each other nor in exactly the same place in their orbitals from unit cell to unit
cell (maybe they are?) when they scatter the photons, they result in interference? What are the
chances that the scattering electrons are exactly in the same place as the electrons in another
unit cell, or of the same phase? And would they not need to be in the same place to sub-angstrom
precision to scatter coherently? I would suggest two possible answers, neither of which am I
entirely satisfied:

1. Something about the crystalline state induces the protein molecules' molecular orbitals to be
totally in synch with each other. This seems too miraculous to be true, in a way. Nevertheless, it
would account for the data, I think.

2. The scattering electrons are elusive probablistic entities which are really no place at all.
This, however, does not solve the problem of the phases (not in the usual sense of finding fourier
phases) which is that it seems unlikely that electrons in multiple unit cells should be exactly in
phase with each other, something which it seems would be necessary to produce interference.

NB this issue came up in a crystallography class several years ago, and I have been ruminating on
it, on and off, since then.

JPK


***********************************
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[log in to unmask]
***********************************

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