when I try to apply patchCTF to negative stain data, the values go beyond 1 and out of the plot and the CTF fit is completely off. Is there a way to fix that?
patch CTF works normally for neg stain data for me. Did you import with “neg stain” toggle on? Is pixel correct? Also, I get better 2D when using “output constantCTF” during import, which means you can skip CTF and go straight to particle picking.
Yes, all is set correctly. I usually do as well constant CTF, but I wanted to see the effect of doing an actual CTF correction
What did you set the amplitude contrast to? Different labs over the years have recommended anything from 0.2 to 0.8 for negative stain data.
I didnt adjust this parameter. I’ll have a look, thanks