Masking out micelles etc - suggestions?

3D Refinement
1

Hi,

Currently it is possible to generate a mask in cryoSPARC, but using it effectively for refinement doesn’t seem possible, unless I am missing something (which is entirely possible, or perhaps likely!).

I am assuming, that if one is refining with a user supplied mask, that the correct option to set for masking is “static”. But if I do that, the results I get are really bad - all kinds of masking artifacts, I am assuming because the mask is being applied from the very beginning of refinement.

I think it might make more sense to allow the user to choose when to apply the generated mask - e.g. at a particular resolution, or at convergence of dynamic masking. I’ve tried playing around with the threshold for dynamic masking, but that has the same issue - a threshold that is appropriate for masking out the micelle/nanodisc in later iterations seems too tight in early iterations. Suggestions/tips welcome!

Cheers
Oli

2

Hi Oli-

For a suggestion, I have found particle subtraction to work well for micelle “masking”.

cheers-

Jon

1 Like
3

Hi all,

Even in cryoSPARC v2, I am having the same effects with masking out the nanodisc as Oli. Is signal subtraction still the only way to mask out the micelle/nanodisc in the current version of cryoSPARC?

Cheers,
Dovile

4

There’s still no way to mask a subregion unfortunately, but non uniform refinement can help quite a lot in such cases. Just be aware that it is not free of overfitting, and resolution can be overestimated, so judge any improvements based upon the appearance of the density map, not the FSC.
Cheers
Oli

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