Hi,
I would like apply tight (but softened) masks around the shape of a protein (rather than the default circular mask) in the raw 2D particle images. I'm wondering how best to do this in Relion, or if another program is more useful here?
Perhaps the best way would be to run a consensus 3D alignment with a 3D mask, then match particle Euler angles with their corresponding 2D projections of the 3D mask (and then multiply the particles with the 2D mask projections to create masked particles).
Alternatively, the process could be achieved just in 2D if one was able to:
1. Simply manually 'draw' a mask in 2D for particular 2D classes.
2. Use a 2D version of a relion_mask_create type procedure to create a 2D mask at a particular 2D density threshold.
Or perhaps there is an easier way?
Any help would be much appreciated!
Cheers,
Joe
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