The Edit Menu

Undo

Recovers the state of the frame before the last operation that you did.

Redo

Re-does the last undo.

Cut

Removes the current selection (or all, if none) from the drawing and puts it into the system clipboard. Paste can be used to use it again.

Copy

Copies the current selection (or all, if none) 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).

Copy as SMILES

Copies the current selection into the system clipboard as smiles only. This is useful if you want to copy to text editors and want the smiles.

Paste

This button puts the content of the system clipboard into the drawing. The system clipboard must either contain a copy from JChemPaint or text in a format JChemPaint can read.

Delete

This button removes the current selection (or all, if none) from the drawing. It is like cut without using the clipboard.

Select all

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

Preferences...

Here you can set some preferences. The dialog has two sections: