<div dir="auto"><div dir="auto">For a detailed look at specimen charging see Chris Russo's paper (<a href="http://doi.org/10.1016/j.ultramic.2018.01.009">doi.org/10.1016/j.ultramic.2018.01.009</a>) </div><div dir="auto"><br></div><div dir="auto">Charging as related to the VPP, see Rado's paper (<a href="http://dx.doi.org/10.1073/pnas.1418377111">dx.doi.org/10.1073/pnas.1418377111</a>) </div><div dir="auto"><br></div><div dir="auto">"Beam irradiation produces positive charges on nonconducting surfaces (21, 22), which leads to phase retardation (22). The phase advance observed here means that the irradiated area has a negative potential, which cannot be a result of beam- induced electrostatic charging."</div><div dir="auto"><br></div><div dir="auto">Happy reading, </div><div dir="auto"><br></div><div dir="auto">Ben </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Mar 24, 2019, 3:00 PM <<a href="mailto:3dem-request@ncmir.ucsd.edu">3dem-request@ncmir.ucsd.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send 3dem mailing list submissions to<br>
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1. Re: ctf-fitting with phase plate (Daniel Asarnow)<br>
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Message: 1<br>
Date: Sat, 23 Mar 2019 12:51:34 -0700<br>
From: Daniel Asarnow <<a href="mailto:asarnow@msg.ucsf.edu" target="_blank" rel="noreferrer">asarnow@msg.ucsf.edu</a>><br>
To: Philip K?ck <<a href="mailto:Philip.Koeck@ki.se" target="_blank" rel="noreferrer">Philip.Koeck@ki.se</a>><br>
Cc: "<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank" rel="noreferrer">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank" rel="noreferrer">3dem@ncmir.ucsd.edu</a>><br>
Subject: Re: [3dem] ctf-fitting with phase plate<br>
Message-ID:<br>
<CALiNCbY15w+-61iDOKXJbXTX5cYkMcMe8Sjb=<a href="mailto:HDBb5gqYFG%2BwQ@mail.gmail.com" target="_blank" rel="noreferrer">HDBb5gqYFG+wQ@mail.gmail.com</a>><br>
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<br>
Hi Philip,<br>
It's just an additional phase added to the argument of the sine and cosine<br>
(amplitude contrast) functions in the CTF. See e.g. Eqn 2. in the CTFFIND4<br>
paper <<a href="http://www.sciencedirect.com/science/article/pii/S1047847715300460" rel="noreferrer noreferrer" target="_blank">http://www.sciencedirect.com/science/article/pii/S1047847715300460</a>>.<br>
It is not dependent on spatial frequency - every frequency gets the same<br>
additional phase shift due to the plate. Here is a gist<br>
<<a href="https://gist.github.com/asarnow/b47c7f1c7aab1d292c10a8c03dd1b6b8" rel="noreferrer noreferrer" target="_blank">https://gist.github.com/asarnow/b47c7f1c7aab1d292c10a8c03dd1b6b8</a>> of a<br>
Python function for evaluating the CTF, which is much the same as those in<br>
Relion or cisTEM.<br>
<br>
I'm not sure if anyone knows the sign of the accumulated charge, but I<br>
imagine electrons are deposited and the charge is negative. Maybe someone<br>
else here has a better physically intuitive argument one way or the other.<br>
<br>
Best,<br>
-da<br>
<br>
On Sat, Mar 23, 2019 at 5:23 AM Philip K?ck <<a href="mailto:Philip.Koeck@ki.se" target="_blank" rel="noreferrer">Philip.Koeck@ki.se</a>> wrote:<br>
<br>
> Hi.<br>
><br>
> I've been looking for information on the contribution of a self charging<br>
> phase plate (hole free or Volta)<br>
> to the argument of the CTF in weak amplitude and phase approximation for<br>
> homogenous specimens.<br>
><br>
> What function is used to describe the phase shift as a function of spatial<br>
> frequency?<br>
><br>
> Also, is the charge produced by the TEM-beam positive or negative (or<br>
> both)?<br>
><br>
> All the best,<br>
><br>
> Philip<br>
><br>
><br>
><br>
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