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

[Philip Köck]

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

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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<mailto: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=DwIF-g&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=DLD4HDmoOaxSOCP0nMGVjblJi9BSsCrU8ugWPw1RCiSQeRIY1zd5FtXPeHBI8PSQ&s=4IOmqVdAw1asPV5ilVPxyWVWa1Ju0oOGUeM8F6AeDIA&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__iubemcenter.indiana.edu&d=DwQFAw&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=o5hWD3mEM1CnBQcA1CoCbNa2ZHuekOPBxJopTggUSnV5bTDS_itRzHiJgm-MqSkZ&s=fCFZWGmlhcc6nzBlB6MWW5ml9YVPIK3FHs7zbhuCqIs&e=>
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