I'm coming in late here, having only now found time to look at the images.
It's facinating, isn't it?
Since the lines are not arcs centered on the origin, this isn't mosaic
spread.
For those who haven't seen the image and the zoom, the diffraction pattern
clearly shows one very long axis and a couple of much shorter ones. The
rotation image is taken rotating around the long one. The small lines are
perpendicular to the long axis, and run fairly uniformly, narrowly and
evenly spaced at the intervals of the reflections along this axis,
throughout the diffraction pattern. Also it appears that this is a
rotation of about a degree; Margriet doesn't give us clues for any of
this.
I'm guessing that whoever said it's a diffuse scatter effect is close to
the mark. I think diffuse scatter comes from the contents of each unit
cell being essentially identical, but that within the molecule things are
waving around a bit (where are Don Caspar and George Phillips when we need
them?). I'll go a touch farther and suggest that it's really disorder --
each unit cell is well aligned to the others, but each one is different in
some way. I'll guess that the RNA decamer is aligned along this long unit
cell axis, but in some way either there's an opportunity for the register
along the RNA axis to slip from one unit cell to the other or each is
rotated slightly.
On the other hand, the fact that there's a wide distribution of
intensities in the Bragg spots, which are quite sharp, is confusing --
there must be a lot of contrast in the averaged structure for this to be
true.
Ok, it's interesting, but I have no idea.
Bob
On Wed, 28 Jan 2009, James Holton wrote:
Hmm. I don't remember that thread. However, I personally think it is a good
idea to keep the "mosaic crystal" as Ewald and Darwin defined it. Just
because current integration software lumps things together into a "mosaicity"
does not mean that every mechanism contributing to the rocking width of a
spot should be given the same name. Especially when it is difficult to
describe the mosaic crystal using any other words. Perhaps Colin could come
up with a cool word for unit cell non-uniformity? Or is he waiting for us to
name it after him? "Nonuniform Anisotropic Variance of Elasticity"? or
"Cells Of Loose INdex"?
Comments and suggestions are welcome.
-James Holton
MAD Scientist
Jacob Keller wrote:
I had thought that in a previous thread, we had all come to a consensus
that actually the largest source of what is normally explained as
"mosaicity" is really differences in unit cell size, due perhaps to uneven
shrinkage in crystals upon freezing or otherwise. I believe that there was
actually an acta cryst paper which investigated all of the various
ingredients of "mosaicity" which supports this (this is why I said it.)
Jacob
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Jacob Pearson Keller
Northwestern University
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