[3dem] Particle shifting issue during alignment

[Behrouz Ghazi Esfahani]

Hello All,
I want to ask if there is any way to limit the particle shift while doing alignment in Relion (or other alternatives?). We have a multimeric protein that we cannot align as the whole complex. We are making progress aligning the monomers after picking them independently. Our problem is that when Cryosparc or Relion refines and classifies the monomer particles it shifts them according to the bigger lob of the monomer and centers on that. We want to see if we can prevent this so the smaller lobe in part of the alignment. The problem is that when the refinements center the particle, the smaller lob will touches the mask edge, but we cannot extract with a larger box size because the neighboring monomers start to come into view.  Thank you!

Best
Behrouz Ghazi Esfahani
PhD Candidate and Graduate Assistant
Stroupe Lab - Cellular and Molecular Biology
Department of Biological Science
Florida State University
Phone: (+1) 850-345-7886
Email: bg19f at my.fsu.edu<mailto:bg19f at my.fsu.edu>

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