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Cambridge Structural Database System

The Cambridge Structural Database System (CSDS) is a package that contains the Cambridge Structural Database (CSD) of crystallographic information on organic and metal-organic compounds containing over 973,000 entries, and a set of software packages to access the database (ConQuest, Mercury, Mogul). ConQuest is the interface to the CSD and is the primary program used for searching and retrieving structural data. Mercury is a visualization tool. Mogul is a knowledge base on molecular geometry. In 2012 we also received SuperStar, a package for predicting protein-ligand interactions using experimental data. With the existing CSD software, Superstar can be run from the command line or from the Hermes interface (see below). We also received the windows only program DASH - which is a program for solving crystal structures from powder diffraction data. If you are interested in installing DASH on any university owned windows system, please contact Anita Orendt. For 2016 and going forward, all current annual academic licensees of the GOLD docking software or of the CSD System will receive a licence for the complete new CSD-Enterprise software suite at no extra cost. As a result all users covered by the licence will be able to use the Cambridge Structural Database (CSD) and as many CCDC-released software products as they want.

  • Version: 2019 release (version 2.0.0 of Conquest, 4.0.0 of Mercury, 5.4.0 of database)
  • Machines: ALL
  • Location: /uufs/chpc.utah.edu/sys/installdir/csd/2019

There is also a web version of ConQuest that can be used from any University of Utah IP address. A CHPC account is not needed to access this version. To access go to webcsd.

In addition there is a web version of IsoStar (a knowledge base of intermolecular interactions stored in the form of scatterplots) that can be accessed at isostar.ccdc.cam.ac.uk/html/isostar.html.

In 2019, CrossMiner was added

 

Information:

To get details of the functionality of CSDS along with access to the User's Guides and Tutorials for the different packages go to www.ccdc.cam.ac.uk/products and www.ccdc.cam.ac.uk/support/documentation.

To Use Conquest and Mercury:

NOTE - January 2019 - Mercury works only on systems with graphics card.  Use from one of the frisco nodes or from a notchpeak interactive node, using the command listed below.  Without the vglrun,  you will get OpenGL errors, and the display window of mercury will not be functional.

You need a CHPC Account to access the CSD installation - see www.chpc.utah.edu/apps/profile/account_request.php to set up an account.

There is a module file in place to set the necessary environment to run the CSDS packages

module load csd

Command to start ConQuest:  vglrun -c proxy cq &

Command to start Mercury:  vglrun -c proxy mercury &

Command to start CrossMiner: vglrun -c proxy crossminer &

Command to start Hermes (interface to run Gold): vglrun -c proxy hermes &

Command to start Mogul: vglrun -c proxy mogul &

Command to start IsoStar clent: run_isostar&

The first time you start ConQuest you may be asked to register. The site number (840) should be filled in, but you may need to add/update the confirmation code (8201C8), and you will now have to also supply your email address. Select register online.

 

Last Updated: 4/17/19