[3dem] [External] Re: tilted transfer functions?

[Daniel Asarnow]

Just to clarify, the patch methods don't require particle locations. The
gCTF method requires particle locations as input but there's no need for
them to be real particles; it too just estimates the CTF on the patches.

David, what do you mean by the goodness of fit estimates being incorrect?
In these methods a goodness of fit measure is used to pick the optimal
defocus values in the patch, and these values do give superior
reconstruction resolution and appear to accurately define the real tilt
axis.

Best,
-da

On Mon, Feb 28, 2022 at 10:51 PM Philip Köck <koeck at kth.se> wrote:

> Hi.
>
>
> There are two separate problems here.
>
> The easier one is to simply determine the defocus in various positions of
> the specimen.
>
> If you only want to work with small cut-outs (such as single particles)
> then you just use the normal CTF-correction with the local defocus. Others
> pointed to software that does that.
>
>
> If you want to work with the image as a whole (for example for 2D
> crystals) the problem is more difficult. Essentially you don't have a CTF
> in that case (it's not a transfer function).
>
> Look at the paper by Ansgar Philippsen (Ultramicroscopy 107 (2007)
> 202–212) if that's what you're after. Also check software for 2D
> crystallography, but I don't what is actually implemented.
>
>
> All the best,
>
>
> Philip
> ------------------------------
> *Från:* 3dem <3dem-bounces at ncmir.ucsd.edu> för Morgan, David Gene <
> dagmorga at indiana.edu>
> *Skickat:* den 28 februari 2022 23:50:32
> *Till:* Daniel Asarnow
> *Kopia:* 3dem at ncmir.ucsd.edu
> *Ämne:* Re: [3dem] [External] Re: tilted transfer functions?
>
> Daniel,
>
> The problem is that the tilt causes the higher resolution Thon rings to
> become out-of-phase, and so the standard programs can't give a decent
> estimate of the goodness of-fit.  I vaguely remember that someone had a
> program that took the tilt into account a number of years ago, but a quick
> hunt for it didn't turn up anything.
>
> --
>     politics is more difficult than physics.
>                                              A. Einstein
>
>             David Gene Morgan
>         Electron Microscopy Center
>              047E Simon Hall
>              IU Bloomington
>           812 856 1457 (office)
>           812 856 3221 (3200)
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> ------------------------------
> *From:* Daniel Asarnow <asarnow at msg.ucsf.edu>
> *Sent:* Monday, February 28, 2022 5:45 PM
> *To:* Morgan, David Gene <dagmorga at indiana.edu>
> *Cc:* 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
> *Subject:* [External] Re: [3dem] tilted transfer functions?
>
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>
> I think any patch-based CTF program, like the one in cryosparc or gCTF's
> local mode (with evenly spaced coordinates instead of real particle
> locations) would work well. With cryoSPARC there's an easy method to plot
> the tilt axis; you can also choose a specific number X and Y divisions for
> the patches.
>
> Best,
> -da
>
> On Mon, Feb 28, 2022 at 2:41 PM Morgan, David Gene <dagmorga at indiana.edu>
> wrote:
>
> Hi,
>
> What's the best way to evaluate the CTF of an image that has a significant
> amount of tilt?
>
> --
>     politics is more difficult than physics.
>                                              A. Einstein
>
>             David Gene Morgan
>         Electron Microscopy Center
>              047E Simon Hall
>              IU Bloomington
>           812 856 1457 (office)
>           812 856 3221 (3200)
>       https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=Xm44kherfjz__BV2RhRKCk-PmcshRB6IONK7QeI8XHTHB2TfKlOfDP5KS-hAzOQu&s=nbJGb2RHerfTraXTBgFzdorrDhdSm7lZSqdOASCTwT8&e= 
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