Average Power Spectra question

Troubleshooting
1

Dear CryoSPARC team, I have a small question regarding the average power spectra job. Apart from using the in-plane angles to align the segments vertically, calculating their PS after padding, and summing those PS, are there any other steps done ? For example, are there any attempts to better align the PS ? I have a strong signal in a PS sum that shouldn’t be there (I know the symmetry), and I’m trying to figure out where it could come from…
Thanks much in advance,
Ambroise

2

Dear @adesfosses,

Thanks for your question. No – as of the latest CryoSPARC version (4.5), nothing else is done – the particles in each 2D class are padded, PS computed, rotationally aligned, and summed together.

Could a possible explanation be related to the 2D class having residual out-of-plane tilt? We have received a feature request to allow 3D alignments in this job for that reason (although this requires a previously refined structure)

Best,
Michael

3

Dear Michael,
thanks for your clear reply. It must come from something else, likely a “contamination” of those classes by segments corresponding to another symmetry (in this case out-of-plane can’t cause this signal). Just wanted to check that there was no attempts to align the PS other than using the existing in-plane rotation.
With best wishes
Ambroise

4

Dear Michael,
are there also not any attempts of “normalizing” the output PS or compensating for amplitude decrease ? I often see stronger signal (white area) at high res than at middle resolution, which is not really as expected, as well as other unusual distribution of grey values across the different resolution ranges. Thanks for confirming :slight_smile:
With best wishes
Ambroise