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

[Michael Radermacher]

David, Daniel

The tilt can be taken into account as described in the CTF correction 
section of the paper on the 3D reconstruction of the V1 ATPase:
Journal of Structural Biology, 135 (2001), 26-37, Materials and Methods. 
May be this is what you are referring to.

Essentially you divide the tilt image into equal patches, determine the 
CTF for each patch, then fit a plane to the CTF values found. The 
equation of this plane then can be used to determine the CTF values of 
each boxed out particle based on its location in the large image, and 
correct the CTF individually.
-- 
_______________
Michael Radermacher, PhD, Prof. Emeritus, FMSA
University of Vermont
Dept. Molecular Physiology and Biophysics
Burlington, VT 05405
Website: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.uvm.edu_-7Emraderma&d=DwID-g&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=5uPib0OSWzEoaC0FE9wYbrgH7TPwpu6dKsmumyxY1p9PNH8Of-IyLYZ_fILF77zA&s=RCyh812VLtPhQ4JFmv5Qr9jPwbc5U0QbEWuVlbQw3VM&e= 

On 2/28/22 11:50 PM, Morgan, David Gene wrote:
> 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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> when clicking links or opening attachments from external sources.
> 
> 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=DwID-g&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=5uPib0OSWzEoaC0FE9wYbrgH7TPwpu6dKsmumyxY1p9PNH8Of-IyLYZ_fILF77zA&s=UAqpQCAtEmUAe-IDHFHuBqLW1x5Q8oNyz08NmP620YM&e= 
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-- 
_______________
Michael Radermacher, PhD, Prof. Emeritus, FMSA
University of Vermont
Dept. Molecular Physiology and Biophysics
Burlington, VT 05405
Website: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.uvm.edu_-7Emraderma&d=DwID-g&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=5uPib0OSWzEoaC0FE9wYbrgH7TPwpu6dKsmumyxY1p9PNH8Of-IyLYZ_fILF77zA&s=RCyh812VLtPhQ4JFmv5Qr9jPwbc5U0QbEWuVlbQw3VM&e=