URL for this document: http://www.lib.uchicago.edu/~atbrooks/strc40.html

Beilstein Structure Searching

Contents of this document:

The Beilstein Database and CrossFire

A brief description of the Beilstein database and the CrossFire search interface (current version 4.0) can be found in the companion guide to this document: Beilstein CrossFire -- Fact Searching

Starting Commander and CrossFire on a Windows Workstation

Use the mouse to point to the Commander icon on the screen and double click the mouse. The Beilstein Commander Screen will display. Click on the CrossFire button to connect to the CrossFire server. If the workstation has been configured properly, there is no need to enter a userid and password.

Figure 1. Beilstein Commander Main Screen

Figure 1. Beilstein Commander Main Screen

The top of the screen displays a menu bar and a function bar; the function bar allows quick selection of frequently used system features. The status bar at the bottom of the screen provides information on the status of the session. To begin double click on the Structure Query box, click the Structure Editor button, or pull down the Task menu and select Structure Editor.

Drawing Chemical Structures

The Structure Editor allows use of the keyboard and mouse to draw a molecular structure that Commander/CrossFire will search in the Beilstein database. The Edit screen (Figure 2) has a menu bar, a function bar, a tool box, and a status bar. The function bar offers quick selection of atoms and bond types and has templates to draw common ring structures. Atom types not shown on the function bar may be specified by choosing Define Atom from the Options menu. Carbon is set as the default atom type; do NOT draw in hydrogen atoms. The tool box appears along the left side of the screen provides a set of tools for drawing, editing, rotating and otherwise manipulating structures.

Figure 2. Structure Editor

Figure 2. Structure Editor Screen

To begin drawing a structure, choose the Edit tool from the tool box (pencil icon). The cursor changes to a pencil when the Edit tool is active in the Structure Editor. Position the cursor in the drawing area. Click and hold down the left mouse button to position an atom. Drag the mouse to the desired end point of the bond; release the mouse button to terminate the bond and place the second atom. The default atom and bond type are carbon and single, respectively. Repeat to continue drawing atoms and bonds. Both atoms and bonds already drawn can be changed at any time by using the Edit tool to click on a bond or atom (the tool shows a "B" or "A" when positioned correctly). In the case of an atom, use the Atom Number box (see Figure 3, upper right popup box)) that appears to change a number of attributes, including degree of substitution at the site, changing the element, hydrogen counts, etc. The bond attributes may be changed in an analogous way using the Define Bond box which opens (see Figure 3, lower left popup box). (Note: Both boxes are shown open in Figure 3; in the Structure Editor, only one or the other may be open)

Figure 3. Changing Atom and Bond Attributes

Figure 3. Changing Atom and Bond Attributes

To erase a portion of a structure that has been drawn, select the Eraser tool from the tool bar. Position the eraser and click on each atom/bond in turn. To erase a larger portion of a molecule, or the entire structure, use the Lasso tool to circle the area to erase and press (or choose Cut from the Edit menu).

Use of templates saves time in drawing complex ring structures. To draw with templates, click on the desired ring in the function bar. More complex templates are available by selecting Templates from the File menu. Once a template is selected, position the Edit tool on the drawing area and click. The template appears in the Structure Editor window and may be moved or resized by manipulating the selected area. Click on the Edit tool when the fragment is positioned satisfactorily to unselect the structure. The resulting structure may be edited further by manual drawing of additional bonds and atoms, changing attributes of atoms and/or bonds, or by combining with other templates to create more complex systems.

Figure 4. Using Templates for Complex Structures

Figure 4. Using Templates for Complex Structures

The CrossFire Structure and Reaction Searching guide provides more information on drawing structures, including how to specify attributes of atoms such as charge, mass, and valency. Steric attributes of bonds my be specified. In addition, it explains how to construct CrossFire sub-structure, Markush, and stereo searches. Reaction searching is also available, but help on creating reaction queries is not provided in this document. Web guides for some of these topics are available from the Chemistry Library Beilstein information page.

Searching and Displaying Database Records

After drawing a structure, click on the Beilstein Commander button in the function bar. This transfers the structure query to Commander which will coordinate the search. The structure query will appear in the right hand box of the Commander introductory screen. Click the Start button (above the structure query box) to initiate the search. Structure searches often take several minutes to complete. If a search goes on too long, or you would like to stop and revise your strategy, click on the Break button in the popup search progress window. If partial search results are available, they may be reviewed and the search strategy refined. After Commander has finished searching the database, a Search Results window will show how many compounds match the search criteria, i.e., how many "hits" in the set. Click Display Hits to view the results; default display is full mode.

Figure 5. Results of Query

Figure 5. Results of Query

The DisplayHits window in full display mode shows the structure of the compound in a smaller window labeled with the Beilstein Registry Number (BRN), the system's unique identifier (see Figure 6).

Some tips for moving through the answer set:

Figure 6. Display of Hitset

Figure 6. Display of Hitset

The full display may be many screens long and slow to update. The display can be customized to show only the information of current interest for each compound. To customize the display of hits, open the Options menu, choose Define User View and select the desired fields from the left side of the window (Figure ). Clear the right hand box by clicking Remove All. Highlight the desired fields on the left and click on Copy to define preferred view; then click OK.

Figure 7. Defining a User View

Figure 6. Defining a User View

Then select User View from the View menu. It is also possible to toggle between the short display (molecular structures only) and the full (or user-defined) view using the Short Display button on the tool bar (symbol on the button is several small boxes).

Printing and Exporting Database Records

Records in the Beilstein database are often many pages in length. To avoid long waits in printing unwanted information, define a User View as described above. While viewing in this mode, choose Print from the File menu and specify the records to be printed. A single record, or sets of results my be printed. Consult the online Help for guidance in using the various print options.

Figure 8. Printing Records

Figure 8 . Printing Records

The Identification information for selected hits may also be exported. Choose Export from the File menu. Identify the record or records to export using the radio buttons, then check the Export Settings (see Figure 9). Depending on the desktop software available, choose appropriate file type (e.g., ASCII delimited text file for importing into Excel).

Other data from the Display Hits screen may be copied and pasted into word processing or email applications. Use the Edit menu (see Figure 6 menu bar) option Copy after highlighting the text desired. Then Paste into another application (e.g., word processing or email). The format of the resulting text varies depending on the applications involved, but the text can be edited after pasting.

Figure 9. Exporting Records

Figure 9. Exporting Records

Logging Off

Exit the Beilstein CrossFire system by choosing File, then Exit from Commander screen. Answer "No" when prompted to save session or results, if you are using a library workstation.

Advanced Beilstein Structure Searching

The structure searching capabilities of CrossFire are impressive and complex. The instructions given here are for basic structure searching. More information by be found in the set of Beilstein CrossFireplusReactions manuals, in other Chemistry Library search guides and in the CrossFire Help menus. Often it takes a good deal of trial and error to develop an effective structure search. Structure queries may be saved to a diskette for future use. (Please don't save them to the hard disk in library workstations). If you are not successful in your structure search, or wish to consult on any aspect of the Beilstein CrossFire system, please contact the Chemistry Librarian.

Andrea Twiss-Brooks
Chemistry Librarian/Chemical Information Specialist
The University of Chicago Library
atbrooks@midway.uchicago.edu
773-702-8777

April 28,1999