Hi all!
I have two questions regarding 3D variability analysis.
After doing 3DVA in cluster mode I took the particles corresponding to the best-looking cluster and run NU refinement. The resulting map looks worst than the map I got from the 3DVA. Why is that happening if both have the same particles? How is refinement in the 3DVA job different from NU refinement?
Since the 3DVA cluster map is looking better than any other map I have, could I use the 3DVA map for publication? How can I get half maps of it? and estimate resolution?
I had a similar problem, with the refinements after the 3DVA maps not being as good.
Specifically, I was trying to increase resolution in a region of interest that moved with respect to the larger part of the complex.
The solution for me was to combine 3DVA and local refinement with constraints, to prevent the 3DVA map from moving too much (I also had to test different approaches of particle subtraction).
I am not sure whether this is exactly your problem, but in that case local refinement might be helpful.