the goodman group
university of cambridge  


   cambridge crystallographic database

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemi cal Information Laboratory
and this information is for historical interest only

Brief Introduction to the Crystallographic Database

The Centre has a WWW server

Quest no longer runs on the older workstations in the SGTL. Consult the upgrade information.


A Simple Search

Getting started: First decide on a name for the files which will hold the results of the search. This name can be any number of letters and numbers, but it must not contain any spaces. In this example, the name filename will be used. Type quest filename.'Quest' is the command to start the searching program. A new window will appear on the screen, which you can position with the mouse. Click the left mouse button to acknowledge the credits, and to move to the Build menus.

Building a substructure: In this example, we will look for all the compounds in the database which contain a certain substructure. You can draw the substructure that you want to search for in the main window, for example, a decalin ring . By default, carbon atoms and single bonds are selected, but you can change this by clicking in the appropriate places. When the substructure is complete, click on Define-Structure. This tells the program to memorise the structure you have drawn. If you want to search for several structures, then you can now draw another, and click Define-Structure when it is complete.

Choose Search options: Now click on To-Search. This will enable you to decide on the information that you want to gather. Choose REFC, ASER, FBIB, FDAT, FCON to remember everything.

Starting the search: Now click on QUEST. This will change all the menus, and show pictures of all the structures you have defined. There should only be one structure, in this example, but it is possible to define several substructures or texts, and combine them in the search with AND, OR and NOT. Click on the structure. This will set up a search question, that will look for every structure in the database that contains this substructure. Now click Start-Search.

During the search: Whenever the program finds a structure that contains the substructure you defined, it will display a 2D picture of the structure, with the substructure highlighted in red. Some structures also have a 3D picture of the structure, which can be rotated and enlarged using the controls at the bottom right of the screen. If the structure is one that you are interested in, then click on KEEP. Otherwise, click REJECT.

Finishing: When the search is complete, data about the structures you kept will be in the files whose names begin with filename. Searching for decalin will find a very large number of structures, and you will probably want to click EXIT before the search is complete.


Notes

  • Holding down the right mouse button is equivalent to repeatedly clicking the left mouse button.
  • Text searches of various sorts are available from the SEARCH menus.
  • The default rotation increment is 30 degrees. Click this number and change it to 2 degrees for smoother rotation.
  • To view a crystal structure in MacroModel, you must convert the file format. You need to have both an FDAT file and a CONN file. These will be called filename.dat and filename.con. Type 'csd2mmod filename' to create a new file filename.mmod.
  • IsoStar is now available



© Goodman Group, 2005-2014; privacy; last updated October 1, 2014

department of chemistry University of Cambridge