Appion

Don't the detail of this. But I learned from Neil yesterday that ACE2 ctf correction would only work accurately with its own estimation.

Sorry, should have also mentioned that I updated the "phaseFlipAceTwo" function in "makestack2.py" so that the necessary parameter file used by ace2correct.exe is generated from db values if no ace2 ctfvalues file exists. I checked this with ctffind values, and it seems to work fine. Don't know if there are other issues that may come up with this though.

ACE2 works best with ACE2
Ctffind works best with Frealign

Craig informed me that there are different interpretations of the CTF equations and it is best to stay within the same package. That said we found little affect on high resolution, just low resolution (100-30A), i.e., the first zero may be off.

Damn, I'm sorry, that's not the functionality I wanted at all. We don't have matlab here, so I couldn't test with ACE1 data. The way I have it now is that all the functions that used to be "getBestAceTwoValueForImage" now call "getBestCtfValueForImage" with the "method=ace2" option, so that it will only look for ace2 values in the database.
I don't know why it's skipping the image if the ACE1 confidence is better, the function shouldn't be looking at any ACE1 data with "method=ace2" set,
I thought line 223 & 224 would skip over anything that's not ACE2 - but does ACE1 also have entries for ['ctfvalues_file'] in the database? that would explain the problem.
if method=='ace2' and ctfvalue['ctfvalues_file'] is None:
continue

No as I see it the getBestAceTwoValueForImage() was changed to getBestCtfValueForImage() and the method is method=self.params['ctfmethod'] on line 472 but self.params['ctfmethod'] is equal to None. Unless I am missing something.

source:trunk/appion/bin/makestack2.py@13869#L469

I see what you mean - my bad. Maybe if "flip-type" is set to ace2image and "ctfmethod" is none, then "ctfmethod" should default to "ace2".
Alternatively we can explicitly output the default "ctfmethod" option from the web. I'm scared to do any svn updates right now - is it safe to svn update these files & make the changes, or would you rather do this?

I would wait until next week to Appion update. We got the whole lab bug testing right now.