3D classification, Regroup 3D classes etc

3D Classification
1

I am a bit confused about what the regroup 3D classes do and what would be best used for.

I did a 3D classification into 10 classes given as inputs a set of symmetry expanded particles (helical symmetry), the 3D volume of the helical reconstruction and a mask to include only one asymmetric in the full complex.
I expected to detect two clear differences in the classes as some asymmetric units in the complex have a bound ligand protein (protein X) and other don’t,. I sort of get that in the classification as at least two classes had the protein bound while the others had variable amounts of occupancy (as judged by the density where protein X would be expected to be). I wanted then to merge the similar classes and further process them. However, I am not sure how to best merge specific 3D classes.Is there a simple way to do this as it is done after 2D classification (with the select 2D classes job)? There is a regroup 3D classes job but I am not sure if this is the right job to select and merge 3D classes after the 3D classification.

Thanks for any clarification

Best

2

You can just use the particle outputs from the classes you want to merge as multiple inputs for a subsequent job - e.g. refinement or reconstruction. This assumes that the classes are in the same orientation though - if it is a case of a ligand binding independently to multiple binding sites on an oligomer, then you might want to rotate some of the classes to match a single reference class. You can do this, if needed, using either volume alignment tools, or Align 3D maps (with the particle input option enabled).

Cheers
Oli