Using mask outputs from refinement jobs for further processing

Cryo-EM Data Processing
1

Hello All,

I was wondering about the mask outputs of NU-refinement, local-refinement, and other similar jobs. What are they generally used for afterwards?

Is it alright to take these jobs’ mask output, crop out some regions that I do not want, e.g. a large blob of noise, and then reupload it to CryoSPARC and use it as a mask for further refinement? Is there anything I need to take into consideration if I choose to do it this way? Or do I strictly need to use the map outputs from the refinement or ab initio and create a mask out of those?

Thanks in advance,

2

Hi @newbie, welcome to the forum!

It’s totally fine to create your own masks however you like, either “from scratch” or by modifying one you’ve already got. The usual caveats apply:

Assuming you’re using CryoSPARC v5, the different mask outputs are explained in the guide page for dynamic masking.

Please let me know what other questions you have and I’ll do my best to answer them!

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3

Hi @rwaldo

Thank you for your detailed answer! It’s perfectly clear now.

Kind regards,

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