Centering auto picked particles

Particle Picking
1

HI All,

I have a couple of questions for the processing starting with -

  1. centering of auto picked particles when using few class averages (of manual picked particles). While the class averages are well centered, a major population of the auto picked is completely off centered. How can we center the particles in cryo SPARC .

  2. how can we set up finer angular steps and shifts in orientation search and refine processes in the reconstruction process.

  3. In the reconstruction process (refine) how can we regulate the
    particle selection based on Figure of Merit or any other criterion to make selection of the best particles from the selected band, suitable for the highest resolution of the density map.

  4. How can I use the un-binned forms of the particles after making selection of the classes of the (class averages) for reconstructions.

Thanks

Andy

2

Did you already try this suggestion?

3

Step size is not a configurable parameter for cryoSPARC 3D refinement jobs. 3D Refinement in cryoSPARC combines stochastic gradient descent with branch-and-bound optimization and therefore should not be thought of as an exhaustive search over particle poses. For details, please see Punjani et al (2017).

4

This likely requires re-extraction of (selected) particles from non-binned, motion-corrected micrographs. The concrete protocol depends on where in the workflow binning occurred.

5

You may want to check out this re-centering particles example for the recently released cryosparc-tools.