[3dem] [TEM] amplitude contrast

Ludtke, Steven J sludtke at bcm.edu
Tue Aug 15 06:49:20 PDT 2017


If you look at electron diffraction for crystals which are 100-500 nm thick, dynamic scattering is, indeed a major issue.

For single particle work, we can get away with approximating the exponential due to either inelastic scattering or multiple elastic scattering as a fixed phase-shift in the CTF. ie - we approximate the exponential as being locally linear. For other domains of CryoEM, the approximation is less good.

On Aug 15, 2017, at 8:05 AM, Philip Koeck <Philip.Koeck at ki.se<mailto:Philip.Koeck at ki.se>> wrote:

***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.
________________________________
Thanks for your answer, Steve.

One clarification: By specimen thickness I meant actual protein thickness, for example 2 layers of catalase rather than 1,
or a long cylindrical molecule in top view rather than side view.
Wouldn’t that lead to a big difference in percent amplitude contrast if amplitude contrast is due to multiple scattering?

Från: Ludtke, Steven J [mailto:sludtke at bcm.edu]
Skickat: den 15 augusti 2017 14:48
Till: Philip Koeck
Kopia: Sacha De Carlo; 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Ämne: Re: [3dem] [TEM] amplitude contrast

If it’s due to multiple scattering, it must depend strongly on specimen thickness.
If it’s due to inelastic scattering, why is it so weak (about 10%)? Inelastic scattering has a larger cross section than elastic, I believe.

Clearly the attenuation of the beam is impacted strongly by specimen thickness. However, the effect you are referring to as amplitude contrast is due to the difference in scattering in one part of the specimen vs another. That is, uniform solvent added above or below the feature producing contrast simply attenuates the beam uniformly, and doesn't produce "contrast".

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu<http://ncmi.bcm.edu>)
Co-Director CIBR Center                          (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)
Baylor College of Medicine
sludtke at bcm.edu<mailto:sludtke at bcm.edu>





-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20170815/e2425bd2/attachment.html>


More information about the 3dem mailing list