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: 2020
  • 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)
  • Using CSD System on Puhti (via NoMachine)
  • WebCSD (limited functionality), point your browser in here

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.

Using CSD on Puhti

Log in via NoMachine, initialize CSD by:

module load ccdc

and you have access to programs ConQuest, Hermes, PreQuest, Vista, Superstar, GOLD, and Mercury.

For example, to access ConQuest, you need to type

cq

or to start Mercury, type

mercury

GOLD has it's own entry.

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 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:

https://www.ccdc.cam.ac.uk/support-and-resources

and e.g. in the FAQ