How to align particles with a given volume

Utilities
1

Hi,

I want to align particles with a ground truth volume generated by atomic model rather than the reconstruct ed map. I wonder how to do only a step of alignment given a map, not the whole refinement job.

BTW, I do not want the map to be lowpassed at the first iteration.

Any advice would help!

2

Have you read this paper?

https://www.pnas.org/doi/full/10.1073/pnas.1314449110

Anyway, the alignments are always there, you can use the ones from the first iteration, and set whatever initial low-pass you want, like Nyquist.

2 Likes
3

I wonder how to use the ones from the first iteration in the “Homogenous Refinement” job?

4

You can select a specific iteration in the Homogeneous Refinement job’s output tab.