Hi Priyanka, I changed the Subject line to something descriptive. Try menu: Actions... Surface... Transparency... [choose the % transparency you want] <http://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions> - OR - Command: transparency 50 (for 50% ... you could use some other number) <http://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html> Another way to make the surface see-through is to use the surface mesh style. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Nov 3, 2020, at 2:19 PM, Priyanka Abeyrathne <pabeyrat@gmail.com> wrote:

Hi ChimeraX developers, Could someone let me know after the superposition of the cryo-EM map in PDB, what is the command to see PDB through the cryo-EM map densities (how to make cryo-EM map transparent without changing domain color in the cryo-EM map to see the PDB)? Thank you. Kind regards, Priyanka