How to mask a certain part in Cryosparc

Hi everyone,

Could anyone show me how to generate or import a mask for certain part of a protein into cryosparc for refinement?



Masking specific regions does not give good results in cryosparc (at least not in the current version).


Hi Jinru, Oli,

As of this evening, we’ve released v2.2 including new beta features for masked local refinement and particle subtraction - you can find a full write-up of the new jobs (including a procedure for mask creation & processing) in the introductory blogpost here.

You can follow the case-study of the yeast tri-snRNP posted here to implement a similar workflow in your datasets where a masked local refinement can improve results. We were excited to see significant improvements in certain datasets, and we’d love to hear your feedback on them.

Happy processing!

Ali H.

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Fantastic!!! Look forward to trying it out :slight_smile:

Hi Ali - has local refinement been tested without signal subtraction? Or is it assumed that there will not be too much signal outside the mask? I have tried local refinement but so far I see “ripply” artefacts near the edge of the mask and a reduction in resolution. Very often in relion I perform masked refinement first, and then signal subtraction of the region outside the mask - is this a viable strategy in cryosparc v2?


From our experience, it is definitely a viable workflow. Doing subtraction before local refinement likely will improve the resolution of the final map, but local refinement without subtraction can also give improvements over the map from consensus refinement.

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