Hi Steven, You have to use the "newMap true" option with "volume zone" (aka "vop zone") for it to create a new map model, rather than just hiding the surface outside the zone. It's explained here, or use command "help volume zone": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone> Then make sure you are actually saving the new map model, not the original one. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 24, 2021, at 11:04 AM, Steven Truong <sdt45@cam.ac.uk> wrote:

Dear ChimeraX Admin., Hello, I was hoping for some help on the save function for an electron-density map (.mrc file). I have a density map (#0) that I trim using:

vop zone #0 nearAtoms #1 range 6

Essentially, I want to remove all the electron density that is not close to my structure (.pdb) #1. Anything farther than 6 angstroms disappears, as expected.

However, when I proceed to do:

save newmap.mrc #0

I get the original map with the electron density I don’t want anymore. It doesn’t seem like I can save the changes to the map, even though I see the changes in the interface. It seems to want to save everything, ignoring the vop command. Is there something else I’m missing here? Thank you for your help, Steven Truong Cambridge University sdt45@cam.ac.uk