4.3 Overlaying Crystal Structures

The ability to overlay crystal structures is only available to registered CSD System subscribers. For further information on obtaining the CSD please see:

http://www.ccdc.cam.ac.uk/contact/obtaining_products/

To perform least-squares overlay of pairs of structures, display the two structures you wish to overlay (see Section 4.2) then select Calculate from the top-level menu followed by Structure Overlay... from the resulting pull-down menu. This will open the Manual Crystal Overlay dialogue.

In the main Mercury window select pairs of atoms from the two crystal structures you wish to overlay (these pairs of atoms will be used to calculate the least-squares overlay). Broken yellow lines will be displayed between each selected pair of atoms:

As pairs of atoms are selected they will be listed in the Manual Crystal Overlay dialogue:

Once the desired number of pairs are selected, hit the Overlay button.

Overlay is performed by moving the second crystal structure relative to the first crystal structure. During overlay crystal structures will be kept rigid, e.g. it is not possible to rotate torsions to find better fits or perform inversions.

Crystal structure overlays can be reversed by selecting Edit from the top-level menu followed by Undo: Overlay from the pull-down menu.

The root-mean-square (RMS) of the pairs of atoms used for the overlay is displayed in the Manual Crystal Overlay dialogue.

To refine the orientation, you can continue to select further pairs of atoms. These will be added to the pairs already listed in the Manual Crystal Overlay dialogue. To remove a pair of atoms hit the Delete button next to the pair you wish to remove. Hit the Overlay button in order to re-calculate the overlay using the current selection.