CreateMaskFromMap

Create Masks from a map

xmipp_threshold -i vol.xmp -o vol.bin -binarize -below "threshold"
xmipp_separate_objects -i vol.bin -o vol

Check the volumes to find the adecuate mask

You can modify the mask with the following program

xmipp_morphology -i vol?????.bin -o vol?????dil.bin -dil

or

xmipp_morphology -i vol?????.bin -o vol?????ero.bin -ero

Apply the mask

xmipp_mask -i vol.xmp -o vol_mask.xmp -mask vol?????.bin

Alternatively,

you may save (and chmod +x) the following script: CreateMask.csh, and execute it as follows:

 ./CreateMask.csh input.vol 0.03 output.vol 

Where 0.03 is the threshold, and output.vol the name of the volume with the mask applied.