I guess you mean you are looking at a CCP4 map at negtaive theshold levels and you see a surface that includes the map box bounds. To see the contours at negative threshold values use the command

On Oct 22, 2024, at 10:09 AM, Stylianos Iliadis via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I want to visualise a surface (isosurface) loaded from a ccp4 file on top of a protein binding site. When I load the volume and adjust the level properly, I can see the “correct” surface (visualised usually on Pymol), but this is only possible when I view slices of the volume=cube box. If I don’t use the sliced view, I only see a cube. Essentially, my question is how can someone hide the “negative” volume inside the cube box that is not part of the depicted isosurface?

Thanks,

Best,
Stel Iliadis

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