You can set parts of the density to 0 using the Map Eraser tool (menu entry Tools / Volume Data / Map Eraser). You drag a sphere over the part you want erased and adjust the sphere radius and press the Erase button. Of course you should not use that if you are going to run analysis that would use that erased density.

Another approach is to just show the density within a certain distance of your atomic models. This is done with the Surface Zone tool (menu entry Tools / Volume Data / Surface Zone). This just hides the surface farther away than the specified distance without modifying the density.

On Apr 30, 2026, at 1:22 PM, Jan Hofmann via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,
I am overlaying electron densities from xplor files with .pdb structures.
The problem is that the .xplor files only crop along X, Y and Z with the vop cover # fbox command.
Is there any command or option to hide some of the xplor densities, but not all?
I have a screenshot attached and would like to hide the density volume circled.
If not, can xplor files be converted into a different file type that allows that?

Thank you.

Best,
Jan Hofmann, M.Sc.
PhD Candidate, Department of Chemistry
Chapman Group
Stony Brook University
jan.hofmann@stonybrook.edu
Office: Room 577, Chemistry

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