Hello, I’m running the 2D classes as before. But this time I cannot see features and most classes have weird bright spots, as shown below
Unnormal classes vs previous classes
What should I adjust to solve this problem? I really appreciate any help you can provide.
Do the new particles come from micrographs that are significantly higher defocus? Or strange background like thick ice? Try selecting your best micrographs only for these parameters and see if you get better 2d
there might be some bad micrographs that contain some funny gray values. if this is true, what you could try is to divide your particles in smaller batches and run a few 2D class jobs separately.
Looks almost like phase plate data when the phase shift is dramatically off.
Also looks like the new data is higher magnification or significantly tighter box around the particles.
Check the CTF fits as well.
Starting with more particles per class might be helpful if all else looks OK.
Yes, better mics are the key to this problem. Thanks for your contribution!