[Jmol-users] dummy atoms included/excluded

[Hens B. <bo...@cm...>]

Rene Kanters wrote:

>I am using JMol to look at Gaussian 03 output and wanted to know 
>whether in a future version JMol will also show dummy atoms. 
>Since I am using z-matrix optimizations, several of the angles that 
>are important to me are defined using a dummy atom.
>
>It looks like JMol uses the standard orientation to parse for the 
>multiple structures in a log file, which has the dummy atoms 
>stripped. If it were to look for the "Z-Matrix orientation:" it  would 
>find the cartesian coordinates of all the atoms.
>The added advantage of using the Z-Matrix orientation is that it will 
>also not flip my molecule around (which the standard orientation 
>sometimes does).
>
>Thanks,
>Rene 
>
On this subject:
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.
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.

Hens Borkent