When I use volume alignment tools to rotate particle sets and corresponding volumes from 3D classification (Class3D is in this case internally downsampling from 300px to 48px), it alters the orientation by a smaller amount than the input value - it still rotates around the appropriate axis (Z in the case I tested), but not by the input amount.
If I reconstruct the 3D class and then rotate the output volume and particle set in the same manner, I get the expected results.
If I reconstruct the 3D class and then rotate the output volume and particle set in the same manner, I get the expected results.
In this workflow, the difference from the first paragraph is that you first use homo/hetero reconstruct to reconstruct the volume at the full box size, and then follow up with volume alignment tools on the output particles/volume?
If I understood correctly, the only difference between first and second workflows is that the first workflow has downsampled volumes fed into the volume alignment tools job, whereas second workflow has full-sized volumes; particles are the same in both cases.
To follow-up, some more questions:
If you take the particles from the problematic volume alignment tools job and reconstruct these: is the map’s orientation consistent with the outputs of the first, or second volume alignment tools jobs described in your post?
In this workflow, the difference from the first paragraph is that you first use homo/hetero reconstruct to reconstruct the volume at the full box size, and then follow up with volume alignment tools on the output particles/volume?
Correct.
If I understood correctly, the only difference between first and second workflows is that the first workflow has downsampled volumes fed into the volume alignment tools job, whereas second workflow has full-sized volumes; particles are the same in both cases.
Yes, that is corrrect.
If you take the particles from the problematic volume alignment tools job and reconstruct these: is the map’s orientation consistent with the outputs of the first, or second volume alignment tools jobs described in your post?
The first - a reconstruction has the same issue, suggesting that for some reason the wrong transform is being applied (even though it is correct in the log)
What is the amount of rotation applied?
90 degrees (pi/2) intended. If performed with the volume from class3d, it looks like ~70 or so (I haven’t measured exactly).
Are you also shifting the volume simultaneously?
No, just rotation around Z
EDIT: I think this is my screwup - rotating a lot of classes and I think I messed up assignments, going to close this for now - sorry!