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

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ALTER IA newval     (nuclear charge of atom IA)
	IA IB newval          (bond length IA-IB)
	IA IB IC newval  (valence angle IA-IB-IC)
	IA IB IC ID newval (dihedral IA-IB-IC-IC)

	Examples:
	 ALTER 10 14.   [change atom 10 to Si (Z = 14)]
	 ALTER  2 5 1.69  [change R(5-8) bond to 1.69A]
	 ALTER  1 2 3 4 180.   [change 1-2-3-4 dihedral
	                          angle to 180 degrees]

	Note that 'ALTER 1 2 3 4 180.' changes ONLY
	the 1-2-3-4 dihedral (often giving unphysical
	distorted geometry).  Use 'TWIST 1 2 3 4 180.'
	to form a proper torsional rotamer.

	Use VFILE to determine which angles can be safely ALTERed.  Otherwise, the coordinates may be re-defined, with unexpected effects on other variables.