Using RELION-4.0 normalised particles in cryoSPARC

Dear all,

I am using RELION-4.0 to extract particles that I plan to later process using RELION and cryoSPARC in parallel. My question is regarding the option in RELION extract job to normalize the particles (Explained in the RELION GUI as: ‘If set to Yes, particles will be normalized in the way RELION prefers it.’). I select ‘Yes’ for this option when using RELION for a later processing but I am wondering if this normalization is also appropriate for particles imported into cryoSPARC.

Thanks in advance for any thoughts on this.


Hi @Andrew yes unless something has changed in recent Relion versions, I believe the normalization in Relion extraction should be correct for importing extracted particles into cryoSPARC as well.
CryoSPARC is somewhat agnostic to the normalization of the particles, as long as all the particles being processed together are normalized the same way. CryoSPARC estimates a noise model and also optimized the greyscale level of input reference maps to refinement jobs in such a way that the overall normalization of the particles does not matter.

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@apunjani, Thanks a lot for the clarification!