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How to Edit Crystal Structures in Free Mercury and Full Licence Mercury

Written by

Sophie Bryant

Posted on

December 6, 2021

This blog explains how to edit crystal structures in both the free and full-licence versions of Mercury.

Chemists and crystallographers can now perform more flexible and efficient structure editing, improving the analysis, visualisation, and interpretation of crystallographic data without requiring a full licence.

Key Takeaways

The free Mercury (in CSD-Community) now supports both Auto Edit (automatic chemistry assignment and hydrogen addition) and Manual Edit (step-by-step structural changes).
These tools simplify routine chemistry and crystallography tasks, saving time and reducing manual effort.
The full licence adds Bond Distance Limit editing, enabling custom bond assignment rules.
Advanced editing supports analysis of disordered structures and coordination geometries.
All editing tools are easily accessed via the “Edit Structure” menu, making workflows intuitive.

Edit a Crystal Structure in Free Mercury

With the free version of Mercury in CSD-Community, you can now edit crystal structures automatically or manually.

Auto Edit: This applies to the whole structure. It assigns chemistry and bond types based on the bond lengths and geometry of the structure. You can add missing hydrogen atoms or identify polymeric structures.

Manual Edit: This allows you to make any change you wish, such as adding or removing an atom, adding or removing a bond, changing an element, or changing a bond type. Each change will be done one by one.

These functions are also available in full-licence Mercury.

Find both the auto and manual edit options in Mercury under the Edit menu, and select “Edit Structure.” You will see tabs for Auto Edit and Manual Edit.

The Auto Edit function in free and full licence Mercury

Edit a Crystal Structure in Mercury

With a full licence to Mercury, you can additionally edit bond distance limits. You can update the bond distances for each possible pair of elements in a structure so that bonds are assigned if the atoms are within this distance.

This allows you to work with disordered structures and explore coordination geometries as well as visualise interactions in a given structure.

To edit bond distance limits in Mercury, go to Edit and select “Edit Structure.” You will see tabs for Auto Edit, Manual Edit, and Bond Distance Limit Edit.