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CSD

The Cambridge Structural Database is a collection of small-molecule organic and organometallic crystal structures determined by X-ray and neutron diffraction techniques.

Available

  • Roihu-CPU: CSD, Version 2026.1
  • Download and install locally

Run module spider ccdc to see module versions and how to load them.

License

CSC provides a national license which allows unlimited installations for academic usage at universities and non-profit research institutes, as well as, access to WebCSD from institutional IP (Internet Protocol) address ranges. Currently, the following universities have access to CSD: Aalto, Helsinki, Oulu, Eastern-Finland, Jyväskylä, Turku, Åbo Akademi, Lappeenranta University of Technology, Finnish Defence Forces University. If you want your university or research institute added, fill in the License agreement and contact us via Service Desk

Using the CSD components requires adhering to these conditions.

Usage

The Cambridge Structural Database System has two major components:

  • The Cambridge Structural Database (CSD)
  • Software for search, retrieval, display and analysis of CSD contents: ConQuest, VISTA, PreQuest, Superstar, Mercury, GOLD, and CSD-CrossMiner.

Software to access and analyse CSD entries:

  • ConQuest search and retrieval software
  • Mercury graphical display, analysis and visualisation of data
  • Hermes Main graphical interface to analysis tools
  • CSD-Editor In-house database creation tools (previously PreQuest)
  • IsoStar A Knowledge Base of Intermolecular Interactions
  • Mogul A Knowledge Base of Molecular Geometry
  • SuperStar Predicting Protein-Ligand interactions using experimental knowledge-base data
  • WebCSD browser access to the CSD database
  • CrossMiner interactive versatile pharmacophore query tool
  • DASH Solving crystal structures from powder diffraction data interactively (only for Windows)

There are three ways to access the CSD System:

  • Local installation (Windows or Linux, takes up a lot of disk space)
  • Using the CSD System via the Roihu web interface
  • WebCSD (limited functionality), point your browser to CCDC webserver

Initialize CSD on Roihu-CPU:

module load ccdc/2026.1

Using CSD as a local installation

A local installation is the recommended way for power users. It works on Windows and Linux. The full installation requires ~18 GB of disk space.

  1. Download the installation media from the CCDC website. The download needs the site number and confirmation code of your university.
  2. Install the software on your computer.
  3. Activate the product with the CCDC Software Activation tool. The activation also needs the site number and confirmation code.

To obtain the required codes, contact either CSC Service Desk or the local CSD administrator at your university. Your university must be covered by the national license (see License).

Using CSD on Roihu via the web interface

The graphical CSD programs run on Roihu in the Roihu web interface (Open OnDemand). You only need a web browser and a CSC user account. Nothing is installed on your computer. Use the Accelerated visualization app.

Note

Use the Accelerated Visualization app, not the Desktop app. See Known issues.

  1. Open the Roihu web interface and log in using your CSC user account.
  2. Open Accelerated Visualization (under Graphical applications). Select the Project and set the resources: Number of CPU cores, Memory (GiB) and Time. Leave Reservation as No reservation. The Partition is vizinteractive, which reserves one GPU (L40).
  3. Launch the app. When the session has started, connect with a web browser (noVNC, Launch Desktop).
  4. In the session, open a terminal and move to a suitable working directory.
  5. Load the CSD module with module load ccdc/2026.1.

Now you have access to CSD programs, e.g. ConQuest, Hermes, Mercury and Mogul. Run them by typing cq, hermes, mercury, or mogul in the terminal, respectively. Note that the GUI (Graphical User Interface) performance can be somewhat slow compared to a local installation.

Billing

The session uses GPU Billing Units: one visualization GPU consumes GPU Billing Units at approximately the same rate as a full CPU node consumes CPU Billing Units. The maximum runtime is 12 hours. Keep the session open only when you are using it, and delete it on the My Interactive Sessions page when you are done.

GOLD has its own entry in Docs CSC.

Using WebCSD directly with a browser

WebCSD has limited functionality compared to the other options. It provides most of the search capabilities.

  1. Use a computer that is within the IP (Internet Protocol) address range of a licensed university. This can be a computer on the campus network or a computer connected through the university VPN.
  2. Point your browser to the WebCSD service.

Access does not need further authentication. If there are problems, contact CSC Service Desk.

Known issues

Mercury does not start in the Desktop app. The error message is error while loading shared libraries: libOpenGL.so.0. The OpenGL library is missing on the Desktop compute nodes. Use the Accelerated Visualization app instead.

ConQuest: "Failed to initialize 3D visualiser". The error in the log file ~/togl_error_init*.log is couldn't choose pixel format. The 3D visualiser does not work in the Accelerated Visualization and Desktop apps. Start ConQuest without it:

module load ccdc/2026.1
cq -no3d

Searches and the 2D structure diagrams work without the 3D visualiser.

The messages qtwebengine_dictionaries and zygote_host_impl_linux.cc ... Permission denied when Mercury starts are harmless.

If the CSD programs ask for activation, load the module first (module load ccdc/2026.1). Do not enter a licence key.

References

New software for searching the Cambridge Structural Database and visualising crystal structures
I. J. Bruno, J. C. Cole, P. R. Edgington, M. Kessler, C. F. Macrae, P. McCabe, J. Pearson and R. Taylor, Acta Crystallogr., B58, 389-397, 2002

Program specific references can be found in each of the online Documentation and Resources

More information