Appion

Defocus input to ctffind4 is in angstroms. Fixed in r19140

Ctffind4 still seems to fail when actual defocus is far from nominal. It seems to convert properly from um to the expected A (see log below) but defocus it found is obviously wrong (see attached screenshot). Looking at the logs it seems to often have strange values for resmax (here 37A; should be 6 as entered) and expected astig (here 83.7; should be 300 as entered)

Defocus search range: 1000 A to 59408 A (0.10 to 5.94 um)
... running ctf estimation at Sun Sep 13 20:10:05 2015
input = 15sep09k_013sq_01hl_04en-a.mrc
output = 15sep09k_013sq_01hl_04en-a-pow.mrc
apix = 1.47
kv = 200.0
cs = 2.0
ampcontrast = 0.07
fieldsize = 1024
resmin = 50.0
resmax = 37.03
defmin = 1000.0
defmax = 59408.9
defstep = 1000.0
expect_astig = 83.7
phase = no
newline =

/usr/local/bin/ctffind4
15sep09k_013sq_01hl_04en-a.mrc
15sep09k_013sq_01hl_04en-a-pow.mrc
1.47
200.0
2.0
0.07
1024
50.0
37.03
1000.0
59408.9
1000.0
83.7
no

ResMax and astig are auto-assigned if using '*Use best values from Database*' is checked to help get a better fit. If you want only you value uncheck the box. For some reason the pop up help is not working the CTFFIND4 page, but it does specify as such on the CTFFIND3 page.

I forgot to include user resmax, so should be better now, so we should have a smarter resmax setting in r19149.

      if ctfvalue is not None and self.params['bestdb'] is True:
         ### set res max from resolution_80_percent
         gmean = (ctfvalue['resolution_80_percent']*ctfvalue['resolution_50_percent']*self.params['resmin'])**(1/3.)
         if gmean < self.params['resmin']:
            # replace only if valid Issue #3291
            self.params['resmax'] = round(gmean,2)
            apDisplay.printColor("Setting resmax to the geometric mean of resolution values", "purple")

The code change in ctfestimate.py probably has wrong indentation. gmean is not defined if self.params['bestdb'] is False. Therefore if gmean < self.params['resmin'] will crash the program.

Thanks for checking Anchi, should be better now.