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 1,016,000 entries, and a set of software packages to access the database (ConQuest, Mercury, Mogul, CrossMiner). 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). For 2016 and going forward, all current annual academic licensees of the GOLD docking software or of the CSD System will receive a license for the complete new CSD-Enterprise software suite at no extra cost. As a result all users covered by the license will be able to use the Cambridge Structural Database (CSD) and as many CCDC-released software products as they want.
- Version: 2021 release (version 2020.3.0 of Conquest, Mercury; 5.42 of database)
- Machines: ALL - but only the frisco nodes for using the graphical interfaces.
- Location: /uufs/chpc.utah.edu/sys/installdir/csd/2021
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 scatter plots) that can be accessed at isostar.ccdc.cam.ac.uk/html/isostar.html.
In 2019, CrossMiner was added
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. 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.
To Use Conquest and Mercury:
NOTE - January 2020: CSD 2021 is now installed. With this version, the graphics requirements allow for this to only be run on the notchpeak interactive nodes or on the frisco nodes. If you run on the kingspeak or lonepeak interactive nodes you will run into errors.
The first time you use the CSD (needed with licensing change made started with CSD 2020:
module load csd
In the window tha appears, select the last tab (Configure local server) and add in
in the window asking for the server host. then select the "configure" button. This should give you a window that says your configuration was successful. You can then proceed to start the different programs as shown below.
For subsequent uses you just:
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 &