I used a mask to exclude the detergent micelle during 3DVA analysis. The mask seems to work in if you look at the result modes. However, after I downloaded output series from 3D Var Display (simple display mode), all of the volumes still contain micelle. Is it a bug? The version that I am using v2.13.2. Thanks.
The mask is only applied during computaiton of the 3D variability components, but we use the unmasked “base” volume (i.e. consensus refinement) when computing the volume series (since the micelle really is present in the images). So this is not a bug - but the micelle region will have no change in it along the series. You can mask each mrc file from the volume series if you wish to remove the micelle completely when visualizing.