The Cambridge Structural Database

Cambridge Crystallographic Data Centre

Hosted by the Caltech Library Services
Access to this library-hosted server or to the locally installable software is limited to Caltech students, faculty, and staff.

The CSD Documentation, Tutorials and User Guides are at http://www.ccdc.cam.ac.uk/support/documentation.

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Current Version Information

Last Updated: Feb. 7, 2014. The 2015 version is expected in February 2015.

CSD System: 2014 release, Version 5.35 Update 1
Database Updates: Feb14
ConQuest: 1.16
IsoStar: 2.2.1
Mercury: 3.3
Mogul: 1.6
PreQuest: 5.35
SuperStar/Hermes: 1.6

Release Notes (Feb. 2014)

There is a known issue with running the CSD software suite under MacOS X 10.9 (Mavericks). Instructions for patching the software to correct these issues are available on the CCDC Support website.

Release Notes (April 2013)

There is a known issue with running Mercury via XWindows on the library server under certain XWindows software versions. If you experience problems, try starting mercury with the command "mercury -mesa" to use the MesaGL graphics library rather than the default OpenGL library.

Release Notes (Dec. 2011)

CCDC/CSD is now available from software.caltech.edu for installation on your own workstation.

The library will continue to run CCDC/CSD system on a library server, with new versions and updates applied as always, for those who prefer not to install locally.

HOWEVER, the library does *not* provide assistance or support for XWindows software, which is required to access the Library's CCDC/CSD server from a PC. The library is cancelling StarNet X-Win32 site license and support, as of 1/1/2012. Note that XWindows is included in most Linux distributions and in MacOS X versions through 10.8. For MacOS X 10.9 (Mavericks) Apple recommends using Xquartz. For Microsoft Windows, there are free alternatives to the StarNet X-Win32 software, such as Xming or Cygwin. If you have any questions about this, please contact software.caltech.edu.

CCDC/CSD is NOT currently available on PC workstations in the Library, due to incompatibilities between the CSD update mechanism and the Library's workstation management software. We hope to be able to remedy this situation soon.

SuperStar has now been made available to all academics. This is a program for generating maps of interaction sites in proteins or around small molecules using data retrieved from IsoStar - also available via CSD. For more information see: http://cds.dl.ac.uk/cds/datasets/crys/csd/superstar/superstar.html.

Mercury has been upgraded and now contains a Data Analysis Module which largely replaces the existing VISTA functionality. This allows numerical and statistical analysis of results from the CSD. For more information see: http://www.ccdc.cam.ac.uk/products/mercury/.


Access to the CSD

There are currently two ways to use the Caltech Library-licensed copy of the Cambridge Crystallographic Data Centre's software and Crystal Structures Database (CSD)



CSD on the Library Server

Access to the Library Server CSD requires setting up an XWindows session on your workstation that connects to the server. Instructions for doing this follow:

Setting Up an XWindows Session on a Macintosh

XWindows software is built into MacOS X through version 10.8. For 10.9 (Mavericks) and later, Apple recommends installing Xquartz.

Open a terminal window (Finder/Go/Utilities/Terminal>. At the prompt, type "ssh -X ccdc.caltech.edu -l ccdc" (that's a lower-case letter L to indicate login username)

If you get a message like this, answer "yes":

The authenticity of host 'ccdc.caltech.edu (131.215.225.16)' can't be established.
RSA key fingerprint is 80:31:37:1e:cd:dc:78:e0:24:ff:af:1b:d9:52:92:25.
Are you sure you want to continue connecting (yes/no)? 

You'll get a password prompt. Enter the ccdc password, available here. You should now be logged into the ccdc server [ccdc@xwin]

At the prompt, type "cq" to start ConQuest, "mercury" for Mercury, "isostar" for IsoStar etc.

Your terminal window may show messages from xwindows like

Warning: untrusted X11 forwarding setup failed: xauth key data not generated
Warning: No xauth data; using fake authentication data for X11 forwarding.
These and similar messages can safely be ignored.

Use the commands below to start the various CSD applications.

Setting Up an XWindows Session on a PC

Starting the various CSD programs from a Windows PC requires use of separate XWindows client software such as the open source programs XMing or Cygwin or the commercial program XWin-32. You must make sure such software is installed on your Windows machine. Start an XWindows session using the instructions for the software you have installed.

Information for XWindows session:

host: ccdc.caltech.edu
login and password: (here)
command: /usr/local/cambridge/bin/cq
name of session: ConQuest (or whatever you want)

Use the commands below to start the various CSD applications.

Using the CSD Applications on the Library Server

CONQUEST

ConQuest is the main searching and retrieval interface to the CSD. It is available on all Caltech Library System (CLS) scanner workstations. Additional information is available here and the ConQuest User Guide and Tutorials are available here.

Using ConQuest on the Library Server

You may run ConQuest on your own desktop provided you use a Caltech IP number and have X server software installed and properly configured.

Create an XWindows session as outlined above. Use the following command:

$ cq

Helpful Tools
ConQuest allows you to save files on the server. To access these files you will need an SSH and/or sFTP client. Login to ccdc.caltech.edu with your SSH / sFTP client, using the same ID and Password as above. Since this is a shared account it is best to create your own subdirectory within /home/ccdc to place your personal files.

ISOSTAR

IsoStar is a knowledge base of intermolecular interactions in the form of scatterplots displayed in a RasMol window. It contains knowledge obtained from the CSD, PDB and theoretical interaction energies. Additional information and IsoStar documentation is available here:

http://www.ccdc.cam.ac.uk/products/knowledge_bases/isostar/.

Using IsoStar on the Library Server
IsoStar and the RasMol client used to display scatterplots are installed on ccdc.caltech.edu. To use them,

Create an XWindows session as outlined above. Use the following command:

$ isostar

The web server and browser on ccdc.caltech.edu are configured to launch RasMol (isorasmol) when a file ending in .istr is accessed. (See the IsoStar Tour via the IsoStar main page for a demonstration.)

SUPERSTAR

SuperStar is a program for generating maps of interaction sites in proteins or around small molecules using experimental information about intermolecular interactions. The Superstar User Guide and Tutorials are available here. More information here:

http://www.ccdc.cam.ac.uk/products/life_sciences/superstar/

Using SuperStar on the Library Server

Create an XWindows session as outlined above. Superstar is now invoked via the "Hermes" application, so you may use either of the following commands:

$ superstar

OR

$ hermes

MERCURY

Mercury offers a comprehensive range of tools for structure visualization and the exploration of crystal packing. More information here:

http://www.ccdc.cam.ac.uk/products/csd_system/mercury/

Using Mercury on the Library Server

Create an XWindows session as outlined above. Use the following command:

$ mercury

MOGUL

Mogul provides easy access to information on the preferred values of bond lengths, valence angles and acyclic torsion angles, using data derived from the CSD. More info: http://www.ccdc.cam.ac.uk/products/csd_system/mogul/

Using Mogul on the Library Server

Create an XWindows session as outlined above. Use the following command:

$ mogul

PREQUEST

PreQuest is a database building program whose primary objective is to create high quality structural data files in a format searchable by ConQuest. PreQuest enables users to build their own private databases of structures that are then searchable either independently of, or in conjunction with, the Cambridge Structural Database (CSD). More info: http://www.ccdc.cam.ac.uk/products/csd_system/prequest/

Using PreQuest on the Library Server

Create an XWindows session as outlined above. Use the following command:

$ prequest


Local Installation

The CCDC/CSD system (programs and database) are available from software.caltech.edu for those who *want* to install and run it on their own workstations. The library will continue to pay for the campus site-license. An IMSS (access.caltech) login and password are required to download the software.

Versions are available for Window XP/Vista/7, for Mac OS X Tiger (10.4) or higher, and for Linux. On Windows 7, a full installation takes about 5GB. Software and database updates are available through a simple "check for updates" mechanism in the Mercury software.

Please see the Server section above for descriptions of the various applications included with the CSD and links to documentation.


Library Workstations

CCDC/CSD is NOT currently available on PC workstations in the Library, due to incompatibilities between the CSD update mechanism and the Library's workstation management software. We hope to be able to remedy this situation soon.


Last Updated: Feb. 7, 2014
Betsy Coles, CSD System Administrator for Caltech Library Services