Particles Show No Motion Trajectories After Reference-Based Motion Correction

Motion Correction
1

I ran reference-based motion correction in CryoSPARC and inspected the example trajectories and example particles. In all of the examples, the particles appear to show no motion at all—the trajectories before and after correction look identical.

Initially, I suspected the issue might be related to the hyperparameters, so I set the hyperparameter search to “Extensive.” However, even after that, I still do not see any difference in the trajectories.

Here are the optimized hyperparameters that were returned:

  • Spatial prior strength: 2.4405 × 10⁻³

  • Spatial correlation distance: 500

  • Acceleration prior strength: 9.4859 × 10⁻⁵

My question is:
If the trajectories are unchanged for all the example micrographs, does this indicate that reference-based motion correction did not actually take effect? Or is it possible for the algorithm to converge to negligible or zero motion even when it is working correctly?

Thanks very much!

J6137_example_particles_0007
J6137_example_particles_00071810×904 66.9 KB

J6137_example_trajectories_0007
J6137_example_trajectories_0007433×423 4.96 KB

2

It is possible, but usually under very specific conditions.

What resolution is your input map? The particles displayed look rather heterogeneous, with no clear features that allow me to quickly say, “yes, OK, they’re different views of the same thing”…

3

I used three maps as inputs for RBMC. They all correspond to the same ~1 MD protein but differ in their binding partners, which range from 50–80 kDa. The map resolutions are between 3.2 Å and 3.8 Å. There are about 20-50 particles per micrograph.

4

likely a fail, to be redone. RBMC zero motion - #2 by hsnyder

5

Thanks for sharing! I am looking back to find a hyperparameter that gives a non-zero trajectory.

6

The problem fixed! Thanks!