the goodman group
university of cambridge  


   use of the ISIS reaction database

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has been replaced by the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

Use of the ISIS Reaction Database at Daresbury


General

The ISIS collection of databases contains over 700,000 reactions. Although this is quite a lot, it is nowhere near comprehensive. It is good to use if you want to search for a type of reaction without being too specific about the exact substituents. The advantage over Beilstein is that searching is usually quite a lot faster. A Tutorial is available. Userids should be obtained by registering on-line at http://cds3.dl.ac.uk/cds/regcds.html. Accounts are available to everyone working in UK academic institutions.

The required software can all be downloaded once you have registered. The ISIS/Base program in the Silicon Graphics Teaching Lab is an earlier version than that available for PCs and Macs. The instructions for the earlier version (in the SGTL) are provided below followed by the differences in the later PC and Mac versions.

Performing a Search in the Silicon Graphics Teaching Lab

The following is a set of instructions for performing a simple reaction search using ISIS. You will see that there are a great many features of the ISIS/Base program that are not described. Extensive Help files can be accessed from within the program and should be sufficient for anyone who wants to know more.

To run ISIS/Base and access the Daresbury database, enter the command "isis". (The command "mdlbase /usr/local/mdl/all.db" which used to be recommended will still work.) Enter your Username in the box. Enter Password in the next box that opens.

The "Reaction Form" should open with the "Query" box highlighted at the top. Double click on the main window. This opens ISIS/Draw for drawing structures.


ISIS/Draw Window

Fig. 1 The ISIS/Draw window as it appears once a reaction has been defined.


Draw the starting material(s) to the left and/or the product(s) to the right. Draw in H atoms at any site where you don't want to allow any substitution but leave them out if you want to allow any substituent at that site.

Select the tool which is an arrowhead surrounded by a square of dots. Click on the first molecule and then, while holding the shift key down, on the other molecules also. Each should get a square of dots around it and a letter beneath. Select "Reaction..." from the "Chem" menu. In the window which opens click on the box where the arrow should be and then click OK. Fig. 1. shows how the screen should appear.

Click on the ISIS Base icon at the top of the tool strip (below File menu) to return to ISIS Base. The reaction you drew should be in the main box. Under "Search" menu click on "Automap Rxn" and then on "By Form" or "RSS" (for Reaction Substructure Search).

When the search is complete, the form will indicate just below the menu bar how many hits have been found and will enter "Browse" mode in order to view the hits. To move from one hit to the next click the up arrow or down arrow on the left of the window. Alternatively click on "#" and enter the hit number you want. The window should look like the following:


ISIS/Base Window

Fig. 2 The ISIS/Base window showing one hit from a search.


To modify the search, click on "Query" mode, double click on the reaction window and edit the reaction in ISIS Draw. Then repeat the search as above.

On Mac or PC

Double click on the ISIS/Base icon to start the program then choose "Open Database" from the "File" menu and double click on "rxl13.db" for PC or "RXN Browser" (may be in RXN Browser folder) for Mac (or maybe "RXL Browser"). It may be that ISIS/Draw needs to be opened manually by double-clicking on its icon before double-clicking on the "Paste Reaction" box to switch from ISIS/Base to ISIS/Draw.

If the latest versions of ISIS Base (2.x.x), ISIS Draw and RXN Browser are installed, you will find they are a bit different from that described above:

1. The first window when you open "RXN Browser" offers the choice of an "Expert Query form" or a "Query Assistant" (see Figs 4 and 5 below). Generally use "Query Assistant". In the next screen click on "Substructure" (i.e. partial structure) or "Full structure" (i.e. exact structure) for reactant and product. Then click on "OK". In the next window double click on the main box to run ISIS/Draw in order to draw the desired reaction.

2. In ISIS Draw the main difference is in defining the reaction (i.e. which molecule is the reactant and which the product). To do this you select the Arrow tool and draw an arrow in the appropriate place on the screen. If there is more than one reactant select the "+" tool and place a + in the appropriate place. To cleck that this will be interpreted correctly click on the icon which shows a tick in the middle of a hexagon (or select "Chem Check" from the "Chemistry" menu). See below, Fig. 3 for a picture of the screen along with instructions.


ISIS/Draw 2.1.3 Window

Fig. 3 The ISIS/Draw 2.1.3 window on a Mac, with instructions.


3. To transfer the reaction you have drawn in ISIS/Draw into the "Paste Reaction" box of ISIS/Base click on the ISIS/Base icon at the top-left corner of the ISIS/Draw screen (just above the lasso icon). You should now see an ISIS/Base window similar to Fig. 4 (Advanced Query) or Fig. 5 (Query Assistant).

Check that the correct search type has been set. The alternatives are "Current Reaction" (i.e. exactly as drawn), "Reaction Substructure", "Same Transformation", and "Similarity". "Automatic Search" does all of these one after the other and so generates the greatest number of hits.
Automapping is normally done automatically but if this is not the case it can be applied by clicking on "Automap" in the top row of buttons in the ISIS/Base window.
Run the search by clicking on "Search" (the right-hand button in the top row).


ISIS/Base Advanced
Query Window

Fig. 4 The ISIS/Base Advanced Query Window on a Mac.



ISIS/Base Query
Assistant Window

Fig. 5 The ISIS/Base Query Assistant Window on a Mac.


4. When browsing through the hits the window is different from the Query mode one (see Fig. 6 below). There are different forms available, which display different selections of information. These can be selected by clicking on the boxes "Summary", "Reference"..."Table" at the top of the form. The "Table" form gives a number of hits, one below the other, and is a quick way of looking through the hits.


ISIS/Base Browse
Hits Window

Fig. 6 The ISIS/Base Browse Hits Window


Older versions for Mac or PC

2. In older versions of "RXN Browser" the Reaction Form was rather different (see below) but for simple searches you still only need to use the "Paste Reaction" box. Automapping is normally done automatically but if this is not the case it can be applied by clicking on "Automap" just above the top right corner of "Paste Reaction" box. Run the search by choosing "By Form" or "RSS" or "Exact Search" from the "Search" menu.


ISIS/Draw 2.1.3 Window

Fig. 7 Older version of the ISIS/Base Query Window on a PC, with instructions on its use.


The window for browsing through the hits was also different in earlier versions. The different forms available, which display different selections of information, can be selected by clicking on the boxes "d1", "d2"..."cl" on the left of the window. The "cl" form is often the default and behaves a bit differently: when it is selected the hits are clustered according to some criterion of similarity; to move from one hit to the next within a cluster click on the up and down arrows at the left of the window but to move to the next cluster click on the "Next Cluster" box above the reaction display box.

Other Databases at Daresbury

The Chemical Database Service at Daresbury also has databases for commercially available chemicals (ACD), protecting groups (SPG), separation of enantiomers (Chirbase) and, for a trial period, solid phase synthesis (SPS) and solid phase organic reactions (SPORE). These are all accessed via ISIS/Base using different browsers. The "ACD Finder" browser is installed on the PWF.
For further details click here.




© Goodman Group, 2005-2017; privacy; last updated November 16, 2017

department of chemistry University of Cambridge