Evgeny,
Yes, you can add dummy atoms using a script. See
http://www.mail-archive.com/jmol-
[email protected]/msg16573.html
for some more info and an example.
You should best use the existing "Xx" notation for an undefined
element. Then you can "select Xx" to act on it, set its size, color,
etc.
Points and lines can be drawn giving their position with atom IDs,
but I'm afraid when you rotate the atoms the drawn objects will not
follow them, you would have to redraw. So you will have to resort to
using the dummy atom itself as a sphere and the bonds you define
(using "connect" command) as lines. Those will rotate
("rotateselected" command").
Not too straightforward, but possible.
Good luck
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