3D Classification - all classes are the same

Hi all, I have tried to do a 3Dclass without alignment after running a NU refinement. The histogram showed that some classification may have been made as the particles are not evenly distributed among classes. However, all volumes from intermediate and final classes are the same. Did I do something wrong, or what could be done to show differences after classification? Do I have do heterogenous refinement after 3D classification? Thanks!

Hello @kpsleung,

Are you checking the output volumes directly from the 3D classification job? I would first try Job: Homogeneous Reconstruction Only - CryoSPARC Guide for each class. This generally has helped me better visualizing small differences between classes.


I find this job type extremely ineffective, even after homo reconstruction of all volumes which is a huge pain. Port to relion for time being

update: try these settings

O-EM learning rate init - 0.75
O-EM learning rate half-life (iters) - 100
Class similarity - 0.25

let us know if it helps (thanks valentin for suggestion)

although in your case it seems you don’t have strong consensus refinement yet. probably have some work to do upstream first (picking, 2D class selection, etc)


Thank you for your suggestions! I have tried again with the settings, and seems that initial classes can converge into fewer ones:

Default setting:

New setting (intermediate plot):

But sometimes the following error hits:

I am now tweaking the parameters to see if classes can be separated with more distinct features / converging into fewer classes, while not hitting any error.

Valentin said this was fixed in a patch. And a new patch came today. Can you update?

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Yep! @kpsleung this bug should be fixed in patch 220118 – this will get applied if you update to our newest patch.

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