This is a really nice GUI. I tried to do supplied masking, following the previous discussion
The process is like this:
1, make_size_map (with input.mrc output.mrc bin_threshold 3.0 interactively)
2, proc3d size_map.mrc output_bin.mrc bin=3
The binarised mask map generated is then very tiny with voxel size (0.004, open in Chimera), compared to true volume (voxel is 1.04). Am I doing wrong?