Department of Chemistry - University of Zurich


Searching the Cambridge Structural Database

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How to get connected to the CSD and start a basic search

On-line documentation for searching the CSD

CSD Homepage

Go to X-ray User Info


The information provided here is intended primarily for members of the Department of Chemistry.

For assistance and questions, please contact Prof. A. Linden (11-E-11, Tel: 5 42 28)

Please delete all unwanted search files when you are finished with them.

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Starting a search

The ConQuest graphical interface is quite intuitive. If you try the various options, you should quickly learn how to construct queries, perform searches and analyse the results. Interactive help and tutorials are available and the on-line manuals should be consulted for detailed information.

Detailed on-line documentation is available. Help is also available during a search, as each window has a HELP menu or button.

If the manuals do not resolve a question, Prof. Linden is always available to assist you. He can also help with any questions that you might have about search strategies.

The command to start a search using the ConQuest software on the Linux Server at the ETH is:

cq or cq -j project (you can also use conquest project)

where project is your projectname. All files subsequently created will carry this name.

If using a local installation of the database, double-click on the ConQuest icon to start the software.

When the cq command is issued, some information will be displayed in a small window and then the main window will apppear. Be patient as the startup may take a little time. From the list of buttons on the left side select the Draw option to sketch a molecule and a new window will be displayed, while the other options allow you to enter various text or numerical information to search on.

In the Draw window, the ADD-3D option can be used to define geometrical tests for the search, so that these features can be analysed, or used later in the structure analysis program Vista. When drawing a fragment, remember that H-atoms are not implicit and you must define them to complete an atom's valency if you do not wish to find all structures with ANY substituent at the incomplete site(s).

Several questions can be built up before starting the search. Search questions do not have to be based solely on structural fragments. Text and numeric strings, such as authors' names, compound names, formula and year are a few examples of possible options. If you wish to develop multiple queries, choose the Store option after creating each individual query (choosing the Search option will start a search directly using the current query only). Multiple questions can be combined using the Combine Queries tab in the main window, e.g. with AND, OR, NOT, etc. You may also specify various options, such as to display only error-free data, or only structures for which atomic coordinates are available, or only organic structures, etc.

Further information is available in the comprehensive on-line documentation.


The search results

During a search with ConQuest, hits will be displayed in a list and you can select any hit and examine it in more detail while the rest of the search is running. Many options are available, including on-screen rotations of a 3D view of the structure and the ability to find bond lengths, angles and torsion angles just by clicking on the relevant atoms. Right-click in the 3D window to activate a menu. To reject any hit, click on the green tick in the list. A question that is too general could give a very large number of hits and the question may need to be defined more restrictively.

Search results will not be saved unless this is specifically requested (you will be warned if you attempt to exit without saving anything). Under the File-menu, a summary PDF file of the search results can be saved. If you want to work further with the atomic coordinates, use the "Export Entries As..." option of the File menu in ConQuest and the primary crystallographic data and atomic coordinates can be exported in CIF or several other formats.


Geometrical analysis of the search results

The program Mercury or the legacy program Vista can be used to analyse the structures you saved during the search, provided some geometrical tests (e.g. bond lengths, angles, torsion angles, etc.) were defined with the ADD-3D button in the DRAW window of ConQuest during the building of the search question. Start Mercury or Vista from within ConQuest under the File-menu: "View in Mercury" or "View in Vista".

It is then possible to get a graphical analysis for various geometrical features, or to graphically look at the information available individually for each entry in the same way that the hits could be viewed during the original search. Thus it is possible to view the molecule in 3D and to rotate it on the screen, as well as look at individual bonding parameters. The full bibliographic data can also be viewed on the 1D screen.


Views of the molecules located during the search

The program Mercury can be used to view, rotate, draw and analyse the structures you saved during the search. This is similar to the 3D viewer available during the search itself, but may be faster when used locally. Mercury for the Mac or Windows PC can be downloaded freely from the CCDC web site. We have a site license to activate some additional features in Mercury. If you want full functionality, please ask Prof. Linden for the license key.

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Searches on the Protein Databank (PDB)

The structural details of proteins larger than 24 residues are not stored in the Cambridge Structural Database, but in a separate database known as the Protein Databank. The PDB can be searched with a web browser.

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Searches on the Nucleic Acids Database (NDB)

The structural details of nucleic acids larger than trinucleotides are not stored in the Cambridge Structural Database, but in a separate database known as the Nucleic Acid Database. The NDB contains structures of oligonucleotides and nucleic acids and can be searched with a web browser. This site also has links to databases containing the structural details of DNA-binding proteins and the structures of nucleic acids determined by NMR.

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Searches on the Inorganic Crystal Structure Database (ICSD)

The structural details of inorganic compounds (i.e. compounds not containing at least one carbon atom) are not stored in the Cambridge Structural Database, but in a separate database known as the Inorganic Crystal Structure Database. The ICSD can be searched with a web browser. Due to license restrictions, the database can only be accessed from a computer whose IP address is within the University's Internet domain (130.60....) or you are using VPN.

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last update: Friday, 09-Dec-2016 13:38:48 CET
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