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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.

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 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.

Available

  • Puhti: 2021
  • Download and install locally

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
  • PreQuest In-house database creation tools
  • IsoStar A Knowledge Base of Intermolecular Interactions (not available on Puhti, please install locally, or use from CCDC)
  • 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 (not available on Puhti)
  • 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 Puhti web interface
  • WebCSD (limited functionality), point your browser to CCDC webserver

Using CSD as a local installation

The installation media can be downloaded from the CCDC website, but needs the site number and confirmation code of your university. After installation you need to activate the product. To obtain the required codes, contact either CSC Service Desk or the local CSD administrator at your university. This is the recommended way for power users. The full installation requires ~18 GB of disk space.

Using CSD on Puhti

Open the Puhti web interface using a web browser and login using your CSC user account.

  1. From there, launch a Desktop.
  2. Open a Host Terminal and move to a suitable working directory.
  3. Load the CSD module with module load ccdc/2021.

Now you have access to the programs ConQuest, Hermes, Mercury and Mogul. Run them by typing cq, hermes, mercury, or mogul in the terminal, respectively. Note that the GUI performance can be somewhat slow as the Puhti web interface does not yet provide accelerated graphics.

GOLD has its own entry in Docs CSC.

Using WebCSD directly with a browser

The WebCSD service provides most of the search capabilities directly via a browser from the computers within the licensed university's IP range. Access does not need further authentication. If there are problems, contact CSC Service Desk.

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

FAQs and useful tutorials can be found at the CSD website and e.g. in the FAQ.

Last edited Tue Apr 5 2022