I have a cell that contains a sphere of organic molecules in a cube of water. What tool and how could I visualize the central cut (slice) of the unit cell? Similar to the one visualized in packmol examples "Double layered spherical vesicle with water inside and outside". Cannot seem to find the right option in VMD. I use macOS and any other tool recommendations are very much appreciated.
I recently used OVITO for this same visualization. There is an option,
Slice, within the quick command search that is available in the free version. You can use it to select the plane at which you'd like to delete from.
If you would like the molecules to still be visible, as in the last packmol example, then after creating the slice open the file again and select
Add to scene. After doing this, use
Select type from the quick command again and select the solvent and delete it with
Delete selected. This should leave you with the sliced box overlayed with the molecules.
In VMD, under "Representations", you can use Cartesian coordinates (among many other options) to select the atoms you want to visualise. For example,
same fragment as (z > 0 and and z < 10) will select all molecules (defined by bond connectivity) for which at least one atom has a z-position between 0 and 10.