Appion

The Ctffind confidence values are on a completely different scale from ACE2's, and none of the same ACE2-style graphs are generated for the viewers. So aside from comparing the reported CTF defoci, a comparison of the results is pretty difficult at the moment. I'm inclined to believe (without any empirical evidence) that using CTFFind values for Frealign reconstructions work better than using ACE2 results, simply because it keeps everything within the same Grigorieff framework. Frealign was written to take CTFFind results, so I don't know if there a subtleties in amplitude estimation or other aspects of the ctf that differ from ACE2 that are important.
It would be spectacular if the same ACE2-style of confidence values & graphical plots were generated for CTFFind runs.

In a related topic, I have never been able to get Ace2 to work on anything other than a couple of images and only after extensive tuning of parameters. I would love to get it working consistently here. Also, I wonder if it is possible to compare the results of doing a reconstruction with the different ways of estimating CTF. As I understand it, makestack will use whichever has the highest confidence value.

FYI the non-ami members of the appion team... Lauren has undertaken to see if we can dig into ctffind and get it to work the way we want. Then she will compare various recons using the various ctf correctors. She is using Niko's rotavirus dataset as a testbed so we should have very high resolution data to test against.

From what I can tell, we are able to do everything with CTFFIND that we want to do (i.e. view the power spectrum in the image viewer and apply ctffind correction to a stack), but it is not as explicit as it could be. In the image viewer, you can view the ctffind split power spectrum by changing "graph1" to "ctffind" on the ACE dropdown menu. This is helpful, but as Bridget said, it would be even better if we could do a side-by-side comparison rather than having to flip back and forth. And even though we can visualize the ctffind estimation, the confidence values are still a problem. I think they should be calculated and reported the same way as ACE for comparison and consistency purposes. However, I am having a hard time figuring out how the confidence values are calculated...does anyone have any insight on this? As for the stack creation, I found that you can apply the ctffind values. After a ctffind estimation is complete, a checkbox to "Only use CTFFIND values" shows up under stack creation. I do not know why this option is not a part of the "Ctf Correct Method" dropdown menu, but instead is located on the opposite side of the form. I think the stack creation page should be reorganized so that all CTF options are grouped together. I will continue looking into and testing these issues, but if anyone has any previous experience or knowledge with this stuff, please let me know.

I'm pretty sure that in Ace the confidence values are simply correlation coefficient between the 1d power spectrum and the modeled CTF power spectrum at the estimated defocus. To do this with ctffind, you would need to know the exact equation Niko uses for CTF.