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Jmol: an open-source Java viewer for chemical structures in 3D

There is a newer version: 14.31.10

LINK IA IB  (draw a 'bond' between atoms IA, IB)\
      Examples:
       LINK 3 17    [draws a 'bond: between atoms 3-17

      Note that this command (unlike FUSE) takes no account of chemical reasonability.