The Atom menu exist as a menu in the main menu and as a context menu, which is available when clicking on an atom. Both are identical except the select/cut/ copy/delete/properties items at the end of the context menu. Both menus set the drawing mode (see Tutorial for an explanation of modes). They both also change some atoms directly, the difference is the main menu does this on selection, the context menu on the item on which you clicked.
These menu items increase or decrease charges of atoms by one.
Here you can show hydrogens on all or no atoms. Note these are settings which can also be achieved by choosing "Explicit Carbons" and "Show implicit hydrogens" in Edit->Preferences.
Changes the isotope of atoms. If only one atom is selected or the context menu is used, you get the isotopes of that element in the submenu. If several atoms are selected, you can choose the difference to the main isotope, which will be calculated for all elements. Note this menu item also changes to the "atom mode", with element and isotope taken from this menu (e. g. you change a carbon to C13, you are then in a mode where you directly draw 13C atoms.
Adds a single electron to an atom or remove one (if any). This makes the atom and the molecule a radical.
Changes the atom(s) to a pseudo atom with a certain label (R, R1..R4). R.. asks you for the label you wish. You also switch to a mode here were you directly draw pseudo atoms.
Changes the atom(s) to a pseudo atom with the * label. You also switch to a mode here were you directly draw * atoms.
Changes the valence of the atom(s). Default is off. You switch to a valence mode after choosing one of the submenus.
These menus set JChemPaint into a mode to set atoms to elements. They all operate the same: Some element is chosen, all selected/highlighted atoms are changed to this and you can change atoms then by clicking on them individually. There are different ways to select the element:
Here you can select the element directly
This opens a periodic table of elements. Hovering over the fields shows additional informations. Clicking on one sets JChemPaint to this element, as if you would have selected it via a menu item directly.
This menu item enables you to enter an element symbol (e. g. "N" or "Cl", capitalisation is not considered) as text. After that, you are again in element mode as if you would have selected a menu directly. If you click on atoms in this mode, the input box appears again. You can then also select from a choice of functional groups to replace the atoms with.
The following menu items only exist in the context menu. They do not switch the mode.
Removes the atom clicked on from the drawing and puts it into the system clipboard. Paste can be used to use it again.
Copies the atom clicked on into the system clipboard. Paste can be used to use it again. JChemPaint uses several formats (SMILES, mol, CML, SVG) so you should also be able to paste it into other programs (depending on abilities of the program).
Removes the atom clicked on from the drawing. It is like cut without using the clipboard.
Selects and marks the atom clicked on, so that it can be deleted, etc.
Selects and marks all atoms and bonds in the molecule, so that it can be rotated, moved, deleted, etc.
Contains submenus for drawing reactions.
Here you can directly set symbol, charge and hydrogen count of the atom clicked on.
Here you can directly set properties (title which will be rendered below the molecule) of the molecule the atom is in.