Jmol as editor
Although Jmol is by design a viewer for molecular structures, its growth has brought some limited capabilities for editing the model. By editing, we mean altering atom positions or identities (e.g. chemical element), addition or removal of some atoms.
Modifying bonds
set autoBond
connect
calculate hBonds
calculate aromatic
calculate structure -- not really bonds
Moving atoms
translateSelected
rotateSelected
invertSelected
minimize
Adding atoms
data
Removing atoms
zap frame
