Cambridge Crystallographic Data Centre

You will need to search the Cambridge crystal structure database for the penicillin and cephalosporin sub-structures. A penicillin search query has been pre-prepared for you;

To invoke the structure editor, click on the rebuild-frag menu item, and then on the T1 query that appears. If you want to start a search immediately, click on T1 and then Start Search.

If you are drawing a molecule from scratch, go to the BUILD menu and select Clear from the menu items. When building a structure using Quest, you will notice that there is no common standard for drawing molecules on screen (unfortunately). With Quest, a click on the screen draws the atom selected (by default C, but in the example below currently S). Further clicks add a further atom to the last atom. If you want the next atom not to be added to the previous, select MOVE first. To convert a single to a double bond, select DOUB, then MOVE and click on the bond desired. To convert a carbon to another atom on the menu, select the type from the screen menu and then MOVE before clicking at the desired atom. If the atom is not present on the menu, click on OTHER. Errors can be corrected using DELATOM or DELBND, or in extremis CLEAR which removes the entire molecule. When you are happy with your structure, click on DEFINE STRUCTURE and then QUEST;


Your defined search operators are shown as T1 (T2 etc). In this case they are sub-structures, but many other definitions are possible, including author names, formulae, etc. It is possible to combine several of these using logical operators. In this case none of this is necessary. Just click on the T1 box to select this item, then START-SEARCH. As soon as a "hit" is found, it is displayed on the screen;



The structure can be rotated using the four small arrows in the bottom right corner of the menu (you might wish to discuss in your writeup the pros and cons of this method compared with those found in other programs; again no common standard applies).

At this point, you have to either KEEP or REJECT the structure before the next one is displayed. If you KEEP the structure, its co-ordinates are written to a file on disk (called penicillin.dat in this case). Continue to the end, when the exit from the database will occur. To perform a further search, type Quest <name of search> from the console window of the workstation, as shown in an earlier diagram above. At any stage you can also go to the alternative 3D projection, in which bond lengths, angles etc can be displayed on the screen.

It is not possible to easily copy any "live" structures from the screen to Claris Works. You can take a "screen snapshot" by pressing the Print Screen key (F13). Drag out a capture area, click on the camera, and then paste the resulting image to Claris.


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©H. S. Rzepa and ICSTM Chemistry Department, 1994-2000.