2D Classification Parameters Help

Hi everyone,

I’m new to 2D classification and am getting weird results in my 2D classifications that I think is happening as a result of my parameters. For reference it is a set of about 400,000 particles. I have a picture for reference as well. Here are my parameters:

Window inner radius: 0
Window outer radius: 0.9
Number of 2D classes: 300
Max resolution: 8
Uncertrainty factor: 2
Circular mask diameter: 180
Recenter 2D classes: on
Recenter mask threshold: 0.2
Force Max over poses/shifts: on
Number of online-EM iterations: 30
Batchsize per class: 200
2D initial scale: 1
2D zeropad factor: 2
Ignore DC from image data: on
Use clamp-solvent to solve 2D classes: on
Use FRC based regularizer: on
Use full FRC: on

Does anyone have insight on how to improve parameters?

Have tried keeping the parameters as default? Leave the mask diameter empty and see what the results look like?



Thanks for the reply. Yesterday I ran with more default settings and got slightly better results that look like the picture below. I was wondering if you had any tips on how to improve 2D classes that look like the ones below. They’re still slightly glossed over with features undefined.

These are not the default parameters - you have “clamp solvent” on, which is rarely helpful. How does it look when you run with the default parameters?

Here are results when i use all default

I would try limiting the resolution used, and test switching the “Force/max” parameter off (so it marginalizes over poses and shifts), as well as increasing the number of iterations (e.g. to 40).

However I’m not sure that’s the issue - your classes look very weird. Maybe double check that all the preprocessing parameters are correct - e.g. Cs, kV, etc?


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Hi @adtaheri, agreed with Oli’s recommendation to check your preprocessing parameters, especially the pixel size you inputted when importing the data. Thanks

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