[3dem] Particle shifting issue during alignment

[Carlos Oscar Sorzano]

Dear Behrouz,

in Xmipp highres (accessible through Scipion) you can say which is the 
maximum shift that should be sought. If you have previous angles from 
Relion or Cryosparc, you may directly import the particles in Scipion 
and refine that alignment.

Kind regards, Carlos Oscar

El 22/08/2022 a las 19:35, Behrouz Ghazi Esfahani escribió:
> 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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