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<div class="">If you look at electron diffraction for crystals which are 100-500 nm thick, dynamic scattering is, indeed a major issue. </div>
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<div class="">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. </div>
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<div class="">On Aug 15, 2017, at 8:05 AM, Philip Koeck <<a href="mailto:Philip.Koeck@ki.se" class="">Philip.Koeck@ki.se</a>> wrote:</div>
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<span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks for your answer, Steve.<o:p class=""></o:p></span></div>
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<span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">One clarification: By specimen thickness I meant actual protein thickness, for example 2 layers of catalase rather than 1,<br class="">
or a long cylindrical molecule in top view rather than side view.<br class="">
Wouldn’t that lead to a big difference in percent amplitude contrast if amplitude contrast is due to multiple scattering?<o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">Från:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class=""><span class="Apple-converted-space"> </span>Ludtke, Steven J [<a href="mailto:sludtke@bcm.edu" style="color: purple; text-decoration: underline;" class="">mailto:sludtke@bcm.edu</a>]<span class="Apple-converted-space"> </span><br class="">
<b class="">Skickat:</b><span class="Apple-converted-space"> </span>den 15 augusti 2017 14:48<br class="">
<b class="">Till:</b><span class="Apple-converted-space"> </span>Philip Koeck<br class="">
<b class="">Kopia:</b><span class="Apple-converted-space"> </span>Sacha De Carlo;<span class="Apple-converted-space"> </span><a href="mailto:3dem@ncmir.ucsd.edu" style="color: purple; text-decoration: underline;" class="">3dem@ncmir.ucsd.edu</a><br class="">
<b class="">Ämne:</b><span class="Apple-converted-space"> </span>Re: [3dem] [TEM] amplitude contrast<o:p class=""></o:p></span></div>
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<span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">If it’s due to multiple scattering, it must depend strongly on specimen thickness.</span><span lang="EN-US" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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.</span><o:p class=""></o:p></div>
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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".</div>
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Steven Ludtke, Ph.D.</div>
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Professor, Dept of Biochemistry and Mol. Biol. (<a href="http://www.bcm.edu/biochem" class="">www.bcm.edu/biochem</a>)</div>
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Co-Director National Center For Macromolecular Imaging <span class="Apple-converted-space"> </span>(<a href="http://ncmi.bcm.edu" class="">ncmi.bcm.edu</a>)</div>
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Co-Director CIBR Center <span class="Apple-converted-space"> </span>(<a href="http://www.bcm.edu/research/cibr" class="">www.bcm.edu/research/cibr</a>)</div>
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Baylor College of Medicine<span class="Apple-converted-space"> </span> <span class="Apple-converted-space"> </span></div>
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<a href="mailto:sludtke@bcm.edu" class="">sludtke@bcm.edu</a></div>
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