[3dem] CTF-correction with phase plate

[Takanori Nakane]

Hi,

In RELION, the phase shift is treated as constant for ALL resolution
shells including very low resolution.

This can cause problems when the VPP developed a lot beyond 90 degrees.
Some people apply high pass filters to fudge this issue.
(see https://www.ncbi.nlm.nih.gov/pubmed/30928614 and
https://www.biorxiv.org/content/10.1101/457861v1)

I am analyzing EMPIAR-10263 to find the best way to deal with
such datasets.

Best regards,

Takanori Nakane

On 2019/05/27 15:34, Philip Köck wrote:
> Is the phase shift due to the PP treated as constant (relative to the 
> unscattered beam) above 20 Angstrom resolution (and as unknown at very 
> low resolution)?
> 
> 
> Philip
> 
> ------------------------------------------------------------------------
> *From:* 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Wim Hagen 
> <hagen at embl.de>
> *Sent:* 27 May 2019 15:49:33
> *To:* microscopy at microscopy.com; 3dem at ncmir.ucsd.edu
> *Subject:* Re: [3dem] CTF-correction with phase plate
> Dear Philip,
> 
> I am not aware of any CTF-estimation package that applies the correct 
> model for a Volta phase plate. The Volta patch to give the un-scattered 
> beam its phase shift has a size I the back focal plane, meaning it gives 
> a soft cut-on, see figure 2B in 
> https://elifesciences.org/articles/23006 . The workaround for this is to 
> start fitting CTF past 20Å. This then requires a nice thin 
> particle-crowded sample to stil successfully fit enough Thon-rings to 
> estimate defocus, astigmatism and the additional phase shift parameter.
> 
> Best,
> 
> Wim
> 
>> On 27. May 2019, at 13:16, Philip Köck <Philip.Koeck at ki.se 
>> <mailto:Philip.Koeck at ki.se>> wrote:
>>
>> Dear all.
>> I'm trying to find out how the contribution of a hole free or Volta 
>> phase plate to the PCTF is described mathematically in various 
>> packages that are used for cryo-EM of macromolecules.
>> The physics behind it would also be of interest.
>> Does anybody know a reference or have some material that can be shared?
>>
>>
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