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Cambridge Structural Database

A powerful and flexible resource to discover the knowledge contained within more than 500,000 crystal structures.

Library Contact

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Yulia Sevryugina
Contact:
3162 Shapiro Library,
919 S. University Ave., Ann Arbor, MI, 48109-1185
7346155694
Website

Install Cambridge Structural Database

Note: Every new release requires a complete re-installation of the software and data. 

The latest installation note can be found here (https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/CSD-ReleaseInstallNotes-2020_1.pdf). 

The installation takes 3 steps: files download, installation, and entering the license information.

Step 1. File Download

  • Option 1: Request the software download links directly from CCDC: http://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/. You will need our site number and confirmation code, and your uniquename@umich.edu email address. Once you submit the request successfully, an email with the download links will be sent to you. (Be sure to check your Spam folder. It may take some time for the email to be sent, it is not immediate.  Please allow for up to an hour.) Follow the links and instructions in the email to download and install the software appropriate to your operating system. Please contact the Chemistry Librarian if you encounter an error message.
  • Option 2: Download files from this DropBox folder

Step 2. Install the Software 

Step 3. Enter License Information

Since we recently installed the license server, two options to configure the new install are available to you:

  • Using node-locked activation key on individual machines: You will need our site number and confirmation code to register for the system after it is installed. Use the software activation tool instead of registering through Mercury.
  • Using the license server: Refer to this page that shows the boxes used for entering license information. Ignore the box on the right.  The box on the left – the one with multiple Tabs along the top -- is the one you want to see. Click on the tab that says "Configure local server". That should bring up a box into which you shall enter the server name and the port number - you will need License Server-assisted activation (Note, that UMich VPN must be running to use the license server).

Troubleshooting:

About the latest release

Cambridge Structural Database (CSD) is a worldwide repository of small molecule crystal structures hosted by Cambridge Crystallographic Data Center (CCDC). The latest release is 2020.3.1. The 2020.3 CSD Release contains 1,076,290 unique structures and 1,097,619 entries (CSD version 5.42).

The latest release note can be found here (https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/CSD-ReleaseInstallNotes-2020_1.pdf). 

The installer contains:

  1. The Cambridge Structural Database, Version 5.42
  2. ConQuest 2020.3
  3. Mercury 2020.3
  4. enCIFer 2020.3
  5. IsoStar 2020.3
  6. Mogul 2020.3
  7. CSD Conformer Generator 2020.3
  8. Hermes 2020.3
  9. GOLD 2020.3
  10. CSD Ligand Overlay 2020.3
  11. SuperStar 2020.3
  12. CSD Python API 3.0.4
  13. DASH 3.4.9 (Windows only, see note about DASH in Changes to Supported Platforms and Products)

Additionally, we have access to other components that are supplied separately:

  1. CSD-CrossMiner 2020.3
  2. WebCSD (accessed via https://webcsd.ccdc.cam.ac.uk)

See the following web page for an overview of what's new across the CSD Software Portfolio over the last 12 months: https://www.ccdc.cam.ac.uk/solutions/whats-new/

The University of Michigan has an unlimited site license to access CSD. You may access the database via either of the following two means.

1. WebCSD - the online portal to the CSD (Click here to access WebCSD)

Read more about WebCSD.

                                                OR
2. Install Cambridge Structural Database System (CSDS) on your own computer. 

Availability of CSDS for different operating systems

If you are running on Windows or Linux, you should be able to install the latest updates seamlessly by simply clicking on Help > Check for Updates in either Mercury or Hermes. If you experience any problems, or you are running on Mac OSX, you will need to download and install the updates manually from the CCDC website: https://www.ccdc.cam.ac.uk/support-and-resources/downloads/​

You can find out more about the updates from this blog article on the CCDC website: https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/csd-2019-updates/

With version 2020.3 as a minimum which is available from the ITAM share you install normally but instead of running the activator you only need to set an environment variable (at least on Linux) to point to the license server.

export CCDC_LICENSING_CONFIGURATION="lf-server;http://license-csd.dsc.umich.edu:8090

CSD Crossminer

You have access to CSD-Crossminer, a tool that allows crystal structure databases such as the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB) to be searched in terms of pharmacophore queries. Intuitive pharmacophore queries describing, among others, protein−ligand interaction patterns, ligand scaffolds, or protein environments can be built and modified interactively. Matching crystal structures are overlaid onto the pharmacophore query and visualised as soon as they are available, enabling the user to quickly modify a hypothesis on the fly. This delivers an overall interactive search experience with application in the areas of interaction searching, scaffold hopping or the identification of novel fragments for specific protein environments.


For example use cases, please see:
Korb O, Kuhn B, Hert J, Taylor N, Cole J, Groom C & Stahl M “Interactive and Versatile Navigation of Structural Databases” J Med Chem, 2016, 59(9):4257, DOI: 10.1021/acs.jmedchem.5b01756.

CSD Python API

This release enables:

• Python 3.7 as the default version for all CSD applications

• The CSD Python API will be Python 3 enabled straightaway at the point of installation 

• Easy integration with other key scientific Python packages

This release will incorporate Python 3 by default, with the miniconda version of the CSD Python API bundled within the 2020.0 CSD Release running on Python 3.7. This means that the CSD Python API will be Python 3 enabled straight away at the point of installation and easy to integrate with other key scientific Python packages like TensorFlow, scikit-learn, matplotlib, pandas and RDKit.

Find out more here: https://www.ccdc.cam.ac.uk/Community/blog/python-3-and-the-csd

For CSD Python API example scripts, download .zip file.