Several have mentioned James to me, and I have had and read a copy for quite some time. I find, however, that the descriptions are more mathematical than mind-pictures. While math is more agnostic, I find mind-pictures more prognostic and helpful to me. But I absolutely love James.
Somebody sent me a pdf with such a mind-picture which describes the origin of the anomalous effect as arising from broken centrosymmetry of the anomalous atoms themselves: (p. 8) "Under normal conditions, electron distributions within atoms are centrosymmetric...Under conditions of anomalous scattering, electrons are perturbed from their centrosymmetric distributions; electrons are jumping between orbitals. The breakdown of centrosymmetry in the scattering atoms is reflected in a loss of centrosymmetry in the pattern of scattered X-ray intensities." http://ocw.mit.edu/courses/chemistry/5-069-crystal-structure-analysis-spring-2010/lecture-notes/anomal_hand1_rev.pdf I had never heard this description before. In a way, this makes great sense and connects the anomalous effect with fluorescence: when one measures anomalous datasets, one is measuring an actively-fluorescing protein crystal. When the atoms fluoresce, they look different to the incident x-ray beam. This also explains why we use fluorescence scans to determine edges empirically. But I am not sure whether all of the dots connect yet; for example, there are many (mostly?) non-centrosymmetric electron distributions in the crystal, and these do not create an anomalous effect. JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: Wednesday, March 11, 2015 12:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Basic Anomalous Scattering Theory Dear Crystallographers, I have had only a vague understanding of what specific things are happening with shell electrons at anomalous edges. Specifically, for example, to what energy of electron-transition does the x-ray k-edge correspond in terms of orbitals, and is that transition energy actually equal to the energy of the photon, suggesting that the photon is absorbed (or disappears?) in elevating the electron? I don't think we say it is absorbed, so how does the energy come back out, from the electron's falling back down, right? So then there's a new photon created, or the same one comes back out? Where was it? Further, I also have heard that the emerging anomalous/resonance photons are of the same wavelength as the incident radiation, but usually there is something lost in transitions (even non-fluorescence ones) I thought? Has it ever been definitively shown that the anomalous photons are of the same energy as the incident radiation? In the case of L-edges, why are there three separate edges? Further, if the resonance occurs when the energies are equal, why does resonance occur at energies greater than the edge? I don't think this happens in other resonance phenomena, or does it? If projects a middle-C-tone into a piano, do all of the lower notes resonate as well, according to the Kramers-Kronig relation? I think it may actually happen in the mammalian cochlea's travelling wave, but is it completely general to resonance phenomena? Just interested, and have wondered these things for a long time in the background of my mind... Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *******************************************
