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Re: [ccp4bb]: Mosaicity-related questions......
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On Monday 10 June 2002 17:10, raji wrote:
> Thanks to all the people who have given me input on my questions
> about high mosaicity and fine slicing. This is the 1st time I am
> handling these weird crystals. Jim's analysis estimates the crystal
> mosaicity to be ~ 0.3 (which is what I also got from Scalepack) while
> I thought the mosaicity was ~ 2.0 or more.
> My crystal has large unit cell dimensions and I was getting overlaps
> @ even 0.2 deg. oscillations. Hence, I thought I could avoid overlaps
> by resorting to finer slicing. Now, in hindsight, I do not know if it
> was the best approach.
If it is just a matter of large unit cell, then overlaps in phi (a.k.a
"z") can be ameliorated by using finer slices. Overlaps in x and/or y
can be ameliorated by moving the detector further back. It can also
help to re-orient your crystal so that the rotation axis is not along a
crystal axis or principle zone.
> Here's some weird features of these crystals
> that have been a subject of discussion in our lab-
> There are quite a few spots that appear to be due to twinning/splits.
OK. So you have a split crystal. Let's call it 2 crystals, that are
nearly but not quite aligned with each other.
> However, there are also several spots that are not predicted at
> mosaicity value 0.3. If I find that I can predict more and more spots
> and maybe, predict most of the spots by increasing the mosaicity
> value in Denzo, what does that tell about my mosaicity?
Possibly nothing, if the increased prediction width is just allowing it
to span the Bragg spots from both crystals. If you were to track the
intensity profile across the full phi width (e.g. by fine slicing as
you tried earlier) you might see a double peak. As phi rotates, the
Bragg reflection from the first crystal goes through the Ewald sphere
and then a fraction of a degree later it is followed by the same Bragg
reflection from the second crystal.
> If the mosaicity is indeed 0.3 and if the xtal is twinned/split,
> then, where do the spots NOT BEING PREDICTED at mosaicity of 0.3
> come from? Are they from the 2nd lattice ?
Probably.
> And, if the spots NOT BEING PREDICTED are from the 2nd lattice, then
> why does Denzo predict more and more spots when I increase the
> mosaicity value ?
Because "mosaicity" is a misleading term in denzo. It is really just a
fudge factor added to the width of the phi slice. If your frame width
(phi slice) is 0.5 degrees and you tell it the "mosaicity" is 0.2
degrees then it will predict all refls whose center lies within (0.5 /
2) + 0.2 degrees from the center of the frame. This allows for true
mosaicity, but it also allows for beam divergence, mis-alignment and
other artifacts of the instrumentation. In your case it is allowing
for the angular offset between crystal 1 and crystal 2.
> If Denzo is able to predict them at higher
> mosaicity, is it possible that those spots are from the same lattice?
It's possible, but from your earlier description it seems they are not.
> How can I resolve unequivocally whether I have low or high mosaicity
> especially when my crystal seems to have some twinning/splitting ?
Look at spot profiles. That is, track the intensity of a single Bragg
peak as a function of phi. If you get a single broad peak then it's
probably mosaicity (or beam divergence). If you get two or more peaks,
maybe resolved from each other maybe not, then it's a split crystal [*]
[*] or else it's some truly odd artifact of the X-ray optics. I have
seen this result from a curved crystal monochromator that was just
about to fail. Essentially it was acting as a not-so-mono-chromator.
But that's not something you normally have to worry about.
--
Ethan A Merritt merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195
phone: (206)543-1421
FAX: (206)685-7002