Biowulf High Performance Computing at the NIH
Cambridge Structural Database/WebCSD
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The Cambridge Structural Database is the world repository of small molecule crystal structures. The database holds bibliographic, 2D chemical and 3D structural results from crystallographic analyses of organics, organometallics and metal complexes. Both X-ray and neutron diffraction studies are included for compounds containing up to ca. 500 atoms (including hydrogens). NOTE: The database is NOW available on the biowulf cluster.

Along with the database are tools for search, retreival, analysis, and display of the CSD contents. These include ConQuest (for text, numeric, 2D substructure and 3D geometric searching) and VISTA (statistical analysis and display of geometric and other data).

WebCSD is also available for all NIH employees interested in using the database.

Installers for Windows, Mac and Linux OSes, are also available for all NIH employees interested in using the software. If you would like to use CSD from your local desktop, please contact staff@hpc.nih.gov, for a link to the download.

Documentation

WebCSD

NIH users can access the CSD directly via the WebCSD portal. New structures are added weekly for up-to-date searches. Users can perform searches - Similarity, Substructure, Text and Numerical - as well as browse the database. The portal is restricted to NIH IP addresses only. If you are at home, you must connect to the NIH VPN before using.

How to Use on Biowulf

CSD requires an X-windows, or preferably NX, session. Click here for more information about X-Windows and NX.

To use, type module load CSD, then quest&, at the prompt.

Sample session: (replace 'username' with your own Helix/Biowulf username).

You cannot run Conquest on the Biowulf login node. You will first need to allocate an interactive session with 'sinteractive'.

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load CSD

[user@cn3144 ~]$  quest &
Starting ConQuest. Use questv5 for QUEST.
Running ConQuest with glibc version 2.5
2.5

The first time you run ConQuest, you will need to accept the license agreement as below. On subsequent runs, you should get the main Conquest window right away.