The Pseudo Atom Menu

Pseudo atoms (created via the Atom Menu) have their own popup menu.

Convert to Regular Atom

This converts a pseudo atom back to regular carbon atom.

Cut

Removes the atom clicked on from the drawing and puts it into the system clipboard. Paste can be used to use it again.

Copy

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).

Delete

Removes the atom clicked on from the drawing. It is like cut without using the clipboard.

Select

Selects and marks the atom clicked on, so that it can be deleted, etc.

Select All

Selects and marks all atoms and bonds in the molecule, so that it can be rotated, moved, deleted, etc.

Reaction

Contains submenus for drawing reactions.

Properties

Here you can directly set properties (label) of the pseudo atom.

Molecule Properties

Here you can directly set properties (title which will be rendered below the molecule) of the molecule the atom is in.