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Hi Dong-Hua, You can use --solvent_mask2 inside relion_refine (where the fact that the average density inside a full capsid is different from outside actually matters), but not inside relion_postprocess. In the latter, you could just provide a single (soft) mask where you mask away both the outer and the inner region of the virus. You can use relion_image_handler to subtract, add and multiple maps (i.e. also masks) together. HTH, Sjors On 07/30/2016 03:10 PM, Dong-Hua Chen wrote: > Dear Sjors and others, > > I wonder if there is any argument in Relion to do inner soft masking (e.g., > to remove DNA or RNA density) for a virus particle in the step of Relion's > Post-processing. > Thanks in advance for your advice! > > Best regards, > Dong-Hua > -- 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