I’m fairly new to ChimeraX so forgive me if I’m a bit ignorant in this question.

I have volumes acquired by tomographic reconstruction of STEM/EDS data (elemental composition in an electron microscope).  I want to visualize several elements together as different colors representing phases.  In some cases, the boundary is fairly obvious and can be represented with an isosurface. 

When I try to set the transparency of the isosurface so I can see the objects inside it, it simply turns darker color rather than transparent.  As an example, here is a silicon isosurface obscuring the other volumes inside it:

For comparison, if I make the isosurface invisible to show the objects inside:

If instead I use the transparency command:

volume #5 transparency 50

The isosurface turns black:

My question is: am I doing this incorrectly?

Thanks,