The PC in the Library has the necessary software and so do the Macs in the PWF (on disk "PWF-CHEM.MAC in folder "Site Specific Software - CH"). There is no version of Beilstein Commander that runs on Silicon Graphics.
The following is a set of instructions for performing a simple structure or reaction search using Beilstein. You will see that there are many features of the 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. Also if you leave the cursor on any 'button' for a couple of seconds an explanation of the function of the button should appear.
On the PWF only: First run the program "Cminst2 Mac" and click on OK in the "Crossfire Client Identification" window that opens. This ensures that the host computer in Manchester can distinguish your workstation from any others on the PWF network that are running Beilstein Commander at the same time.
Run the Beilstein Commander program and then choose "Crossfire" from the "Application" menu (or click the icon on the menu-bar with the crossed red arrows). If the "Crossfire Server Profile" window opens click on OK. When prompted enter your ATHENS username and password.
If connection with the host computer is not successful, check the settings
by selecting "Connections" from the "Options" menu. The required settings
are:
Under "Server"
Host: crossfire.mcc.ac.uk
OS: AIX
Program: /xfire/bin
Root: /xfire
Under "Communication"
Port: XFIRE
Port Number: 8001
After the connection with the host computer in Manchester has been established, double click on the structure box. This runs a program called "Structure Editor". To draw molecules select the pencil tool on the left-hand strip and drag the cursor across the screen to draw each bond. It is easiest to select the type of bond (single, double, triple) and the atom to go on the end from the tool bar above the window before you draw the bond. (If you want to change the type of a bond or atom that is already drawn, then select the bond or atom type desired and hold down the Shift key while you click on the atom or bond to be changed.)
There are two ways to allow various substituents at different positions of
the molecule (i.e. to do a substructure search):
(i) With the pencil tool selected click once on an atom. This will open a
window and you can change the setting of "Free sites" for that atom from
"0" to "1", "2", etc. or "MAX".
(ii) Draw in explicit H atoms at every site that you do not want
substitution and later when you return to Beilstein Commander you can set
the option "implicit free sites" for the whole structure.
If you want to do a structure search, then click on the ">BC" box to return to Beilstein Commander (or choose Beilstein Commander from the "Task" menu).
If you want to do a reaction search, then draw both the reactant and product. Select "Reaction" from the "Editmode" menu. Click on the Select tool (dotted rectangle) or the Lasso tool. Double click anywhere on the reactant to select the whole molecule and click on the "Reactant" box on the bar above the structure. In the same way select the whole of the product molecule and click on the "Product" box. The screen should then look as shown in Fig. 1 below.
Fig. 1 The Beilstein Structure Editor Window with a reaction query defined.
Once the reaction is defined, return to Beilstein Commander as described above. The window should look similar to Fig. 2 below.
If you want to allow any substituent on atoms where the H atom(s) have not been explicitly drawn in then click on "Options" above the main structures window and then click the box for "implicit free sites" in the window that opens. Then click "OK".
Select the database you want to search. "BS9902ABAB" is the latest issue of Beilstein, which is for organic compounds. Alternatively the Gmelin database contains inorganic and organometallic compounds. Click on the "Start" box to begin the search.
Fig. 2 The Reaction Query window of Beilstein Commander on a Mac.
When the search is complete (which may take some time) a window appears to say how many hits have been found. Click on "Display Hits", which runs the "Display Hits" program. The first hit will be displayed (see Fig. 3). To see the structural diagram (if it is not already there) as well as the text, select "Include structures" from the "View" menu. Alternatively choose "Structure" from the "View" menu to show the stucture only and "All Fields" to show the text only.
For each hit there may be some more text below the visible text; use the scroll bar at the right to scroll through all the text. Each compound and each literature reference has its own underlined reference number. If you click on this a new window will appear. For a compound this window will give references for all reactions in the database involving that compound and also references for looking up spectroscopic and other data on the compound. For a literature reference the new window gives the abstract and details of all substances used and all reactions performed.
Fig. 3 The Display Hits window of Beilstein Commander on a Mac after a reaction search.
