I've had this confusion before and one of the recent threads in jmol-users 
has brought it again, so I have a suggestion to improve the doc.

http://chemapps.stolaf.edu/jmol/docs/#hover
says:

[...] "Any other parameter or string is used as the label, which can contain 
atom property fields such as %a or %U." [...]

I suggest adding this:
[...] "Any other parameter or string is used as the label, which can contain 
atom property fields such as %a or %U and will apply to all atoms in the 
model. To set a specific hover label for one atom, select the atom(s) and 
then use 'set hoverLabel' <red link>." [...]

(I believe this is a correct description --if not, please ammend)




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