Pseudo atoms (created via the Atom Menu) have their own popup menu.
This converts a pseudo atom back to regular carbon atom.
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 properties (label) of the pseudo atom.
Here you can directly set properties (title which will be rendered below the molecule) of the molecule the atom is in.