12.1 Manually Editing a Structure

To manually edit a structure, hit the Modify button in the top-level menu and select Edit Structure... from the resulting pull-down menu. This will launch the Edit Structure dialogue:

Within this window you can choose to:

Add hydrogen atoms: click on the Hydrogen Atoms button, select the number of required hydrogen atoms, then click on the atom(s) to which hydrogens are to be added.

Add bonds: click on the Bonds button, choose the bond type from the pull-down menu, then click on the two atoms that you wish to be bonded.

Remove atoms and bonds: click on the Atoms & Bonds button, then pick on the atoms or bonds you wish to remove.

Remove complete molecules: click on the Molecules button, then pick an atom or bond from within the molecule you wish to remove. It is also possible to only remove a particular copy of a molecule (see Section 11.8).

Edit a bond type: click on the Set Bond Type to button, choose the bond type from the pull-down menu, then pick the bond(s) you wish to change.

Molecules can be broken apart by the deletion of bonds.

New bonds may join together two separate molecules in a single structure. However, you can not add a bond between two different structures (when in multiple structure mode). Nor can you join together symmetry related molecules, for example if packing is turned on.

When reading structures from the Cambridge Structural Database, all Suppressed Atoms are treated as being in a single molecule. Using remove Molecules therefore provides an easy way to remove all suppressed atoms from within a structure.