CrystalMaker makes it easy for you to show or hide groups of atoms, either by direct selection (select a group of atoms, then right-click in the Graphics pane to display a contextual menu and choose: the Hide Selection), or via the "Vis" checkboxes in the Atoms Inspector.
If you wish to hide all atoms of a particular kind (e.g., all hydrogen atoms in an organic structure), simply locate the relevant element row in the Atoms Inspector (this is the row with a disclosure triangle and an element symbol), then uncheck the Vis checkbox. All sites with that element symbol will now be hidden.
You can also use the Atoms Inspector to hide all atoms that reside on a particular crystallographic site (e.g., the "T1" site in a feldspar mineral): this time, locate the relevant site row (you may need to open up some element rows to find the site row) and uncheck the site's Vis checkbox.
Did you know? Use the Atoms Inspector's Actions or contextual menus to quickly expand or contract the element groups on display. You can also sort by element symbol, visibility, atomic radius, coordination - and even colour! To display the contextual menu, simply right click (control click on a Mac) in a blank area of the Atoms Inspector.