Clownfish like mode 0


Could anyone explain why 3D variability analysis returns a clownfish like mode 0 (see attached) as a result with mode 1 showing actual domain movement? Mode 1 also makes biological sense.

The particle stack of up to 750000 particles yields a 4 A map in uniform refinement and to around 3.4 A in NU refinement.
Is the data somehow noisy and is this noise not accounted for?

Best Regards
Yehudi Bloch

Dear Yehudi,

I have also seen this before, I always assumed it is because there is no movement to be detected in this mode (whether that is because of the settings of the job or biologically true is another question).

Happy to know if I am wrong!

Hi @ybloch, thanks for reporting and good question. We do sometimes see these kinds of results. The best known explanation is that in your data, there is a variation that is not motion/heterogeneity but something systematic (e.g., misaligned particles, junk particles, incorrectly CTF estimated particles, etc) and 3DVA picks up this variation as best it. It’s unclear how to get rid of this but seeing a mode like this doesn’t invalidate the other modes of variability you may see.

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