Re: [Jmol-users] dummy atoms included/excluded

[Miguel <mi...@jm...>]

Hens wrote:

> There are two sides to this: Jmol *is* showing dummy atoms when they
> appear in XYZ files, and I didn't find a simple command to *exclude*
> them from the display.
> Did I overlook something?
> It would be convenient if they could be addressed by the element name
> 'dummy' or by the atom type X / Xx / XX.

You should be able to select them using the element name "unknown".

I don't really like 'dummy' because Jmol turns any unrecognized element
into 'unknown'.

However, if you think that something other than 'unknown' is more
appropriate, then please let me know.

-- 1 minute later --

Actually, I forgot that I could easily add 'dummy' as an alias for
'unknown', so it is not a problem. I just made the change and it will be
in the next release.

You should also be able to select them as 'select elemno=0'

Note that I have not tried either of these things. If they do not work
then let me know.


> Miguel: a dummy atom is a point in space on a position where there is no
> atom, but which is convenient to include in the definition of the
> positions of real atoms, or a group of real atoms.
> Example: one can write the structure of cyclopropane very efficiently in
> internal coordinates ( z-matrix) using the center of the ring as the
> origin, i.e. by placing a dummy atom there.
> Or: to measure the distance to a benzene ring, one could take the center
> of the ring as a reference point.

OK. Thanks.


Miguel