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These are defaults, which can be redefined. Note that while entering text on the command line, some of these control keys take on text editing functions instead (CTRL - A, E, and K, and DELETE), so you should clear the command line before trying to edit atoms.
CTRL-C Replace picked atom with carbon (C) CTRL-N Replace picked atom with nitrogen (N) CTRL-O Replace picked atom with oxygen (O) CTRL-S Replace picked atom with sulpher (S) CTRL-G Replace picked atom with hydrogen (H) CTRL-F Replace picked atom with fluorene (F) CTRL-L Replace picked atom with chlorine (Cl) CTRL-B Replace picked atom with bromine (Br) CTRL-I Replace picked atom with iodine (I)
CTRL-J Set charge on picked atom to -1 CTRL-K Set charge on picked atom to +1 CTRL-D Remove atom or bond (DELETE works too). CTRL-Y Add a hydrogen to the current atom CTRL-R Adjust hydrogens on atom/bond to match valence. CTRL-E Inverts the picked stereo center, but you must first indicate the constant portions with the (lb) and (rb) selections. CTRL-T Connect atoms in the (lb) and (rb) selections. CTRL-W Cycle the bond valence on the picked bond.
UNDO and REDO of conformational changes (not atom changes!)
CTRL-Z undo the previous conformational change. (you can not currently undo atom modifications). CTRL-A redo the previous conformational change.