Hi Michael,
thank you for the reply.
- mask range: the mask was indeed ranged from -0.0325 to 0.4.
I noticed for the resizing in cryosparc I had left out the threshold option.
I re-ran my volume tools job, with threshold set to 0.05 this time. I downloaded the map, and chimera now showed a range of 0-1.
I re-ran the particle subtraction with this new mask and the particles looked similar to before.
So I ran a 2D classification, and yay!
I have a dark blotch in the center of the classes (see attached).
That is what I should get, correct?
As I checked everything:
2) Particle scales look ok.
3) Inner/outer radii are always the same (0.85 and 0.99 for the local refinement job with the subtraction mask, and for the subtraction job).
Looks like my mask was the problem.
Thanks a lot!
Kind regards,
Luca
