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How to Use Mercury for Crystal Structure Visualization and Analysis
Mercury is a software developed by the Cambridge Crystallographic Data Centre (CCDC) that allows users to view, analyze, and understand molecular structures and their properties. Mercury can display crystal structures in various ways, such as ellipsoids, polyhedra, packing diagrams, Miller planes, voids, and BFDH morphologies. It can also show intermolecular contacts, such as hydrogen bonds, and calculate simulated diffraction patterns. Mercury can be used to explore published structures from the Cambridge Structural Database (CSD), as well as proprietary structures from common file formats.
In this article, we will explain how to use Mercury for crystal structure visualization and analysis, and what are the benefits of using the full licence version over the free version. We will also provide some tips on how to optimize your Mercury experience and avoid common pitfalls.
How to Download and Install Mercury
Mercury is available in two versions: the free version through CSD-Community, and the licensed version through CCDC's software suites. The free version offers an abridged list of functionalities and access to a teaching subset of the CSD. The licensed version provides access to the full CSD - over 1.1 million structures - and extra functionality including molecule and structure editing and the visualization of voids.
To download the free version of Mercury, you need to register for a CSD-Community account on the CCDC website[^1^]. Once you have logged in, you can go to the Free Mercury page[^1^] and click on the Download Free Mercury button. You will be asked to fill in a short form with some details about yourself and your intended use of Mercury. After submitting the form, you will receive an email with a link to download the installer for your operating system (Windows, Mac OS X, or Linux).
To download the licensed version of Mercury, you need to purchase one of CCDC's software suites that include Mercury: CSD-Core, CSD-Discovery, CSD-Materials, CSD-Particle, or CSD-Theory. You can request a demo or a quote on the CCDC website[^2^]. Once you have purchased a software suite, you will receive an email with a link to download the installer for your operating system and a licence key to activate your software.
To install Mercury, you need to run the installer and follow the instructions on the screen. You may need to agree to some terms and conditions and choose a destination folder for your installation. If you are installing the licensed version of Mercury, you will also need to enter your licence key when prompted. After the installation is complete, you can launch Mercury from your Start menu (Windows) or Applications folder (Mac OS X).
How to Load and Display Structures in Mercury
Mercury can load structural data from a variety of formats, such as CIF, MOL, MOL2, PDB, AUX, etc. You can load structures from your local files or from online databases such as the CSD or PubChem. To load a structure from a file, you can either drag and drop it into the Mercury window or use the File > Open menu option. To load a structure from an online database, you can use the File > Retrieve menu option and enter a search term or an identifier.
Once you have loaded a structure in Mercury, you can display it in different ways using the toolbar buttons or the View menu options. You can choose from various display styles such as ball-and-stick, space-filling,
wireframe, etc. You can also show or hide different features such as labels,
symmetry elements,
unit cell axes,
etc. You can rotate,
translate,
zoom,
or measure
the structure using your mouse or keyboard shortcuts.
Mercury has a comprehensive range of tools for 3D structure visualization and exploration of crystal packing. You can generate packing diagrams of any number of unit cells in any direction using the Packing Diagram tool. You can define and visualize least-squares planes
and Miller planes
using the Plane tool. You can take a slice through a crystal in any direction using the Slice tool. You can calculate simulated diffraction patterns for any displayed crystal structure using the Diffraction tool.
How to Analyze Structures and Properties in Mercury
Mercury has several features that allow users to analyze structures and properties ec8f644aee