CTF correction

[Reza Khayat]

Hi,

I am still a bit confused about CTF correction for STA. The tutorials indicate that correction is performed during refinement; however, my CTF extract log file writes:

CTF information exists. Will do phase flipping..

Is this text incorrect or correct? Perhaps its a remenant of an earlier version of EMAN2.99? 

I'm running EMAN2.99.66

EMAN 2.99.66 ( GITHUB: 2025-01-25 22:09 - commit: 08d5c0a83 )
Your EMAN2 is running on: Linux-5.4.0-171-generic-x86_64-with-glibc2.31 5.4.0-171-generic
Your Python version is: 3.12.8

I'm concerned cause my resolution is stuck near the first-zero (calculated using Wen's CTF simulation web-site). However, my concern may be inappropriate as I have less than 100 particles so the CTF correction may not be all that impactful...

Best wishes,

Reza 

[Steve Ludtke]

If you've followed the process normally, then accurate per particle per tilt defocus information is available at subtilt extraction time. If my memory serves (we've gone through a lot of variations in STA over time), the particle tilts are individually phase flipped based on this information during extraction. If you do a "c" step during refinement, which generally doesn't do much, I'm guessing it unflips the phase, then flips again with the new CTF?  I'd have to read through the code to double check, but I don't think you're seeing anything wrong here. 

Having said that, if you are getting stuck at the first zero, it is possible that the automatic defocus estimation has not worked well for some reason. It is dependent on there being enough contrast and the specimen being a reasonable thickness. It is possible to do some manual checking of the determined defocus to see if things generally seem to match up properly. However, with only 100 particles, it probably isn't reasonable to expect much resolution...  We'd need a lot more information to really assess.

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