VEGA ZZ can add, remove and change atoms.
6.1.1 Add atom
Selecting Edit Add Atom it's possible to add one or more new atoms:
To add a new atom, choose the Element, the Hybridization and the Bond type, thus click the atom to which to connect it. You can specify where to place the new atom in the atom list choosing After the selected atom, At the residue end, At the molecule end. If you want to select an element not included in the Element box, click Other and put the element name in the Selected field.
If the bond type isn't shown in the main window, open the View settings and make it sure that the Multivector item in the Wireframe tab is checked.
6.1.2 Remove atom
If you want to remove one or more atoms, you can select the Edit Remove Atoms item in the main menu or click the Remove button of Add/remove atom dialog box.
Click the atom and it will be removed automatically.
6.1.3 Change atom
To change the atom properties, you can select Edit Change Atom/residue/chain menu item.