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Hi Sameer, We've seen similar effects sometimes. An even softer mask might help, or otherwise subtracting the regions you're masking out from the experimental images (like we did in eLife 2015 paper on gamma-secretase, see Methods section there) mmay also help. HTH, Sjors > Hi, > > I'm using a soft mask to locally classify a smaller region of a 3D volume > using the 3D classification option in Relion. While this is working, I'm > also seeing some strong extra densities in the result, which clearly do > not belong to the 3D structure. These densities appear as blobs or craters > towards the edges of the area that was masked. I was wondering why we see > these densities, and is there a way to prevent their generation. > > I'm using relion_mask_create to create the soft mask, as follows > > relion_mask_create --i input.mrc --o outputmask.mrc --ini_threshold 0.0071 > --extend_inimask 4 --width_soft_edge 4 > > Thank you very much. > > Best, > Sameer > > ________________ > Sameer Singh, PhD > Albert Einstein College of Medicine > 1300 Morris Park Avenue > New York, NY - 10461 > Phone: 718-430-2048 > Cell: 917-848-9319 > -- Sjors Scheres MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44 (0)1223 267061 http://www2.mrc-lmb.cam.ac.uk/groups/scheres