[3dem] 3dem Digest, Vol 148, Issue 8

[Anchi Cheng]

Hi, Farzad,

Most of your questions are discussed in Glaeser et.al. JSB 174 (2011) 1-10.
I also did a series of experiments to see how coma affects single particle analysis
outcome in JSB 204 (2018) 270-275.

What I would recommend is that you do make your measurement of the convergence angle.
Not taking a guess.  The value you quoted is a small enough number that with averaging of particles
they won’t have obvious effect.  However, it is not to say whether you have
other lens aberration that will affect your results.

As far as beam convergence affecting pixel size, that is indeed true, but coma effect (i.e. phase shift, dip
in FSC etc.) will be seen at much smaller convergence angle before you can tell from pixel size change.

Anchi Cheng

> On Dec 6, 2019, at 12:00 PM, 3dem-request at ncmir.ucsd.edu wrote:
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> Today's Topics:
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>   1. Parallel Beam Illumination (Farzad)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Fri, 6 Dec 2019 10:00:28 +0100
> From: Farzad <farzaad at gmail.com>
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Parallel Beam Illumination
> Message-ID:
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> 
> Dear Friends and Colleagues,
> 
> We have a JEOL JEM 3200 FSC, a 300keV TEM with cryo-stage and energy
> filter. This microscope has just 2 condenser  lenses. I mean there is no
> even condenser micro/mini-lens and and no objective micro/mini-lens and
> after the condenser system we have just a twin lens type objective lens.
> 
> This classical optical system means that your smallest beam diameter in
> parallel beam is equal to the smallest C2 aperture and for avoiding
> irradiation we have to converge the beam a bit. I have not yet measured the
> convergence angle but it should be maximum around 100 n.Rad in worse case.
> We use objective lens wobbling for making the axis of the cone of the beam
> parallel to the optical axis and not more.
> 
> My questions are as follows:
> 
> 1- what would be the effect of this deviation from the beam parallelism on
> the Phase Contrast? I always read it leads to a general phase shift (it
> means but not contrast?).
> 
> 2- What is the effect of this deviation from the bam parallelism on the
> resolution? My first guess would be we will have coma on the edges of the
> image.
> 
> 3- What are the other problems with beam convergence? Somebody told me it
> may affect pixel size accuracy, but I could not get a valid argument for
> that yet.
> 
> I would appreciate if you can share your knowledge on the beam parallelism
> issue in cryo-microscopy here.
> 
> Kind Regards,
> 
> Farzad Hamdi
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