Noisy 3DVA representation


My 3DVA result in simple mode is very noisy(attached). Does anyone know what can cause this problem? How should I optimize the parameters?


Hi @Ty22!

It looks like this map is at a relatively low contour, does it still look noisy if you increase the contour level?

Also, the simple mode is not a true reconstruction of your particles. The volumes from simple mode have the difference volume for that component simply scaled by the coordinate, then added to the consensus volume. This means that any noise in the difference volume will be scaled as well, which can make the extremes noisier than coordinates closer to zero. This problem can be somewhat mitigated by using the Intermediates mode instead, which does perform a reconstruction of your actual particles, but reconstructions from smaller numbers of particles will have their own noise problems.

Please let me know if you have any more questions!