The Connection Editor

The Connection Editor can be used to determine whether proper atom ordering is maintained throughout a molecule group. You can also use it to automatically reorder atoms to align atom tags between related structures across a molecule group (useful for preparing structures for QST2 and QST3 transition structure optimizations). Manual atom reordering is also possible.

Figure 30. The Connection Editor
The Connection Editor is used to verify and assign atom equivalencies in two molecular structures. When working with a molecule group, viewing in multi-geometry mode allows easier comparison and editing. In this contrived example, we need to swap the ordering of atoms 3 and 4 in one of the models in order for the atoms to correspond properly. This can be done by clicking on the Enable Autofixing button or via a manual process.

When the Connection Editor is active, the molecule will be analyzed to determine if the atom tags match across the entire molecule group, and the status bar will report the result. If potentially fixable mismatches are detected, the dialog will report this and suggest that the user "Enable Autofixing." Clicking on the corresponding button will tell the Connection Editor to reorder the atom labels to remove these mismatches. The success or failure of autofixing will be reported on the status bar. When autofixing is active, any manual reordering of atom tags will cause autofixing to be called and remove any mismatches that might have been introduced.

Atoms can also be manually reordered by using the mouse. These operations use a reference atom as their basis (see the first bullet):

• Left clicking: Designate the atom as the reference atom. This can also be done using the Reference Atom control.

• Middle clicking: Assign the tag one greater than the reference's item to the selected atom.

• Right clicking: Swap tags with the atom and the reference atom. The atom then becomes the new reference atom.

The Apply to Molecule Group checkbox determine whether the Connection Editor's actions apply only to the current model or to all models within the molecule group.

The ZMat Tools popup allows you to perform some Z-matrix operations on the molecule or molecule group:

• Sort H: Move hydrogen atoms to the end of the atom ordering.

• Reorder: Reapply standard Z-matrix ordering.

• Reconnect: Regenerate connectivity data.

The other items on this popup menu do not apply to Gaussian.