IndexError when selecting 1 component of 3DVA in cluster display

Hey All,
My cryosparc version is v3.3.1. One component of my 3DVA represented another conformation of my target protein in simple series mode. Thus, I want to fitler these partcles out from the whole dataset by using cluster display mode. I selected ‘Only use these components: 0’ and only the component was loaded into analysis but an Error was reported after cluster particles as:
File “cryosparc_worker/cryosparc_compute/”, line 85, in
File “cryosparc_worker/cryosparc_compute/jobs/var3D/”, line 320, in
IndexError: index 1 is out of bounds for axis 1 with size 1

anyone has some idea about it? Thank you very much.

Hi @ChemJ,

We do indeed assume we have at least 2 components for the clustering job. The clustering itself (based on Gaussian Mixture models) will still work on 1 component, but our standard plotting will not. We can fix this in an upcoming release.

In the meantime, perhaps using Intermediates mode with component 0 will suffice? This will effectively cluster the particles based on several equally sized (overlapping) regions along that component dimension.


Hi @ChemJ, you can do this, you just need to replace the other components with your desired component (so it is effectively clustering self vs self) using the low level results interface.


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@ChemJ The fix is included in release 3.3.2.


Hi @wtempel Thank you for this nice update! I’ll have a trial and compare with the result from the intermediate mode as @vperetroukhin suggested.