[Jmol-developers] dummy atoms + z-matrix

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

Rene wrote:

> A dummy atom is an atom that is does not have a nucleus or electrons,
> in other words it really is just a place holder in space that can be
> used as a reference point to define bonds, angles, and torsions in a
> z-matrix.

This sounds familiar ... at least one person has told me this before ...
but I manage to forget

> In a geometry optimization using a z-matrix the z-matrix orientation is
> in the output which has the dummies in them: they have an atomic number
> of -1. The standard orientation, I believe, is the one you parse for
> and that one only real atoms, not dummies. Enclosed is an output file
> that shows some of this (x.log).

I see that in your Gaussian 03 output and in k2.xyz that the dummy atom is
identified as element 'X' ...

Q: Is 'X' *always* used as the element symbol for dummy atoms for *all*
programs?

> About the representation, I believe that JMol already has that set up.
> The problem I had is that they are not recognized in a G03 z-matrix
> optimization file. Enclosed is the concatenation of the xyz files that
> NWChem gives for one of my calculations. The dummy atom is the pink one
> between the two carbons.

Any element symbol that Jmol does not recognize currently gets mapped to
element 0 whose name is 'Xx' ... It is large, pink, and has large covalent
bonding radius so that it is easy to see. I intended it to be used mostly
for debugging.

> This actually is also could work as an example
> about my question of the graph. What I was wondering there is the
> possibility to have, for instance, a measurement like a CH bond
> distance be graphed against a CCH angle in the molecule (to look for
> correlation in their motion). This, of course, only works for a
> multistep file.

It sounds like this would be a good thing for someone to add to the Jmol
application, either embedded or as a plug-in.

> Does this provide you with what you need wanted to know?

There are two related items that probably should be addressed at the same
time.

1. Lone pair support ... another 'strange' non-element point.

2. Z-matrix support ... everyone says that it is easy, but I haven't done
it yet.


None of these things is going to happen until after the official v10 release.


Miguel



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Open Source Molecular Visualization
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