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Contents of this document:
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About
the Beilstein Database and CrossFire
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The Beilstein CrossFire search system is a client interface that
provides access to the CrossFire search and retrieval software and
links structure, reaction, text and numeric data in the Beilstein
and Gmelin databases. The Beilstein database contains information
on more than 8 million organic compounds and associated chemical
and physical properties and 5 million chemical reactions. There
are more than 30 million numeric and text reports arranged in some
300 fields, all of which are searchable. The Gmelin database covers
more than 1.4 million organometallic and inorganic compounds (including
coordination compounds, alloys, glasses, ceramics, polymers and
minerals), with more than 800 property fields defined. Searchable
data fields include Chemical Abstracts Service (CAS) Registry Numbers,
chemical names, molecular formulae, boiling point, spectral parameters,
solubility, dissociation constants, thermodynamic data, dipole moments,
and reaction conditions. Historical coverage in both Beilstein and
Gmelin are particular strengths of the databases, with references
to the chemical literature back to the 1770's. Print predecessors
to these databases are Beilstein Handbuch der Organischen Chemie
and Gmelin Handbuch der Anorganischen Chemie.
This document is intended to introduce new users of the database
to some basic search techniques; those who have complex search needs
will find additional documentation in manuals provided by Beilstein
Information Systems (copies available in the Chemistry Library Office),
in more advanced guides on the Beilstein
information page or from the Help feature in the CrossFire/Commander
menu. Users at the University of Chicago may use CrossFire at library
public workstations in the Chemistry and Crerar Libraries, or may
download the software client for use on their own networked machines.
At this time, there is no option for off-campus remote access. For
more information on downloading the client, point your browser to
the Beilstein
information page on the Chemistry Library web site, or contact
the Chemistry Librarian.
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Login to CrossFire
On a machine where CrossFire/Commander has been installed you
should see a Beilstein 2K icon. Double click on the Beilstein
2K icon on the computer desktop to start CrossFire: |
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The main Beilstein Commander window will appear. Click on the
crossed red arrow icon to login (see Figure 1). If the
workstation has been properly configured, login should proceed automatically
with no need to enter a loginid or password. If you are prompted for
a loginid and password, contact the Chemistry
Librarian for instructions. Note that the top of the screen displays
a menu bar and a function button bar. The function button bar are
shortcuts; all functions are also available from the drop down menu
bar. |
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Figure 1.
Logging into CrossFire from the Beilstein Commander window
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| To begin a structure search, either click the Structure drawing
button simply double click in the box on the right side of the
screen. The Structure Editor will open in a new window. |
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Drawing
Chemical Structures
| The Structure Editor provides tools for drawing using both
keyboard and mouse operations. The resulting structure query (or structure
based reaction query) will be transferred back to the main Commander
search window. The Structure Editor has a menu bar, a function
bar, a tool template, and a status bar (see Figure 2). The function
bar offers quick selection of common atom and bond types and has common
ring templates. Using these shortcuts will result in atoms and bonds
having the default characteristics defined. Changes to these characteristics
(e.g., valency, free sites, bond order) are made using Define Atoms
or Define Bonds from the Options menu, or with the Pencil
tool. |
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Figure 2.
The Structure Editor menu, function, tool and status bars
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To begin drawing, choose the Edit (Pencil) tool. The cursor
will change to a pencil  when
this tool is active. 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 left mouse
button to terminate the bond and position the second atom. The default
atom is carbon and the default bond type is single. Repeat the click,
hold, drag, drop sequence to draw additional atoms and bonds. It
is probably easiest to draw all atoms as carbon and all bonds as
single until the basic structural shape is established and then
edit the structure to indicate non-carbon atoms (or groups) and
other types of bonds. Common rings may be added to the drawing by
using the Ring Bar buttons on the upper right side of the
Structure Editor display; use the Edit (Pencil) tool
to connect the ring to the base structure.
Atoms and bonds in the structure can be changed at any time using
the Edit (Pencil) tool. Position the tool over the atom to
be changed; tool is positioned correctly when A (atom selected)
or B (bond selected) appears in the middle of the pencil
(see Figure 3).
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Figure 3. Structure drawing with atom selection (A pencil) or
bond selection (B pencil) activated
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With the desired portion of the structure targeted this way
(i.e., either A or B shows on the pencil tool), click to activate
the appropriate menu box. Change bond order, stereochemistry,
ring/chain topology for bonds. Specify number of free sites,
charges, element symbol for the atom, hydrogen counts at that
atom, ring/chain topology of the atom. Look carefully at the
display of the structure after changing the various options
-- free sites will be marked with an asterisk *, changes in
bond order may result in dashed lines, generic groups will appear
as alpha symbols on the structure. Remember, for substructure
searches, the default setting for an atom is unsubstituted;
any desired free site must be specified explicitly.
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Figure 4. Bond attributes menu
box |
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Figure 5. Atom attributes menu
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The Atom Attributes function can also be used to specify
a number of generic group substituents in a substructure search.
Select the Symbol drop down menu and scroll down to the
Generics option. Clicking on this choice will bring up
a Generic group selection menu (see Figure 6). The type
of group can be displayed by pointing to the generic group symbol
with the cursor (without clicking). Select the desired symbol
by highlighting and click OK. |
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Figure 6. Using the generic groups
in the Structure Editor
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For complex structures, it may be easier to use one of the templates
provided in the software and modify the base structure. Using
the menu bar in the Structure Editor, select File,
then Group Template. A selection window will open with
a number of choices for the template files (which have a file
extension .BSD) (see Figure 7). |
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Figure 7. Opening a group template file
in the Structure Editor
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Scroll through the resulting graphical display of template structures
(see Figure 8) to choose the base structure desired. Double
clicking on the structure will paste the template into the Structure
Editor (including stereochemistry). This base can then be
modified using the Drawing Tool (Pencil) or the Atom
and Bond Attributes functions.
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Figure 8. Selecting a group template
file and choosing a base structure
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Some basic tips for drawing structures for valid queries:
Once the structure query is completed, transfer the query to the Beilstein
Commander window by clicking the Go to Commander button  .
Click the Start Search button to run the structure query.
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Searching
Structures and Displaying Results
Once the search has completed, a Query Result window will
pop up. The number of substances matching the query will be displayed
(e.g., 138 substances as shown in Figure 9).
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Figure 9.
Query Result Window Showing Number of Substances Matching the Search
Query
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There are a number of predefined display options available, in addition
to the ability to create individual customized displays. Full database
records may be extremely long, slow to load for viewing, and even
slower to print out (some records are more than 100 printed pages).
Use of predefined or customized (User View) displays results
in much shorter records for viewing and printing. If the predefined
options are not sufficient, it will be necessary to create customized
displays.
Predefined Display Options:
Click on Display Hits button in the Query Result window
to look at the substance records. Select View from the menu
bar in the resulting Display Hits window to switch to a different
display option. There are four main predefined displays that are
available (Short Display, Identification, Hit Only
and All Fields) as shown in Figure 10.
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| Short Display |
Displays hits as structures in a grid. Number of rows
and columns displayed can be changed under Options (on menu
bar), then Select Short Rows and Columns. Useful for scanning
quickly through a set of compounds. |
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| Identification and Include Field Availability |
Recommended display (see Figure 11) for quickly
browsing through a result set to see the types of data available for
each compound. Once the fields of interest are determined, select
All Fields from the View menu or create a customized
User View including those fields to see the data. |
| Hit Only |
Identification fields (name, formula, registry
numbers), references and specific data fields that matched the query
entered (e.g., only 13C NMR data displayed for the query shown in
Figure 8). Select Highlight Hits to see matches of search
terms in the display. |
| All Fields |
Full record display. Select Include Field Availability
and use underlined codes (hyperlinks)
to jump to desired sections of the record. This format NOT
recommended for printing and/or exporting records! |
Figure 10.
View Menu Options and Predefined Views
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Customized User View Display Options:
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If predefined formats are not appropriate
for specific display, printing and/or saving requirements, create a customized
User View. There are two menu/function steps: Options/Define User
View and View/User View. To Define User View follow the
steps outlined in Figure 11. After finding and copying fields of
interest, click OK to return to the Display Hits window. The
new customized view will not be displayed yet -- to activate the customized
view, be sure to select User View from the View drop down
menu (Figure 10).
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Figure 11. Define a User View |
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Once a view (predefined or user defined) has been selected, use the buttons
at the top of the Display Hits window to navigate through the compound
hit set and to navigate back and forth from reaction and reference displays.
The most useful buttons are explained in Figure 13.
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Figure 12. Navigation Buttons for Display Hits Window |
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Tips for navigating hit sets:
- Underlined numbers in various colors are hyperlinks to other
compounds, literature citations or reactions. To navigate back from
a hyperlink, use the special previous and next (white) arrows.
- Jump back to the top of a record using the Top hyperlinks in
the compound records.
- Switch structure display on or off using the Structure On/Off
button. The structure window may also be resized to make it smaller
for easier viewing of the record, or larger to see structural details.
- If viewing hit set for preparations (remember to choose Display
As: Reactions on the Commander screen before starting the search),
be sure to Structure On to see a graphical display of the reaction.
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Printing and Exporting/Saving Results
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When printing or saving records from hit sets, the current display setting
is the default setting for the printed or saved records. Therefore, if
All Fields is selected, the entire record will be printed or saved,
often resulting in dozens of pages of unwanted information and/or extremely
large saved files. Use a shorter predefined or customized display to create
smaller print jobs and files.
If printing, verify that the desired display is active, and choose File/Print
to further customize the print job output. A Print window (Figure
13) will pop up; modify the settings as desired for the print job
using the radio buttons on the left side and the bar buttons on the right
side. If a range of hits is desired, be sure to select the range; the
default is only to print the record currently showing in the Display
Hits window.
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Figure 13.
Print Options Window |
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Exporting records for use in other applications is not a trivial matter.
Specific export parameters must be defined by the user, and novice users
with little knowledge of data export/import procedures may encounter difficulties.
Beilstein CrossFire 2000 does provide some guidance, in the form
of an Export Wizard (Figure 14). Delimited files created
using this wizard may be imported into a variety of software, including
non-chemical applications like Excel. In general, most occasional users
will find it more convenient to print out desired data than to spend time
figuring out the export process. Regular users may find that the ability
to save and reuse export settings will be worth the effort. Consult the
online help or contact the Chemistry
Librarian for assistance if the Export Wizard does not provide
enough guidance.
Alternatively, it is possible to copy and paste fields from the Display
Hits window into any text editor. Use the mouse to highlight the desired
text, select Edit/Copy. Paste the selection into the text editor
and save the text file. The resulting text will be encoded as HTML; change
the .txt in the filename to .htm and use a browser to view the results.
This method will be time consuming for large hitsets, but for a few compounds
provides perfectly acceptable results.
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Figure 14.
The Export Wizard Introductory Screen for Creating Reusable Export
Settings
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Logging Off |
Exit the Beilstein system by choosing File/Exit from the menu
bar in the Commander window. When using any library workstations,
answer No when asked if the search and results are to be saved. (Users
may choose to save searches on their own machines; these searches and hitsets
can be rerun and redisplayed in future sessions). If the Structure Editor
window was opened, it will need to be closed manually; all other Beilstein
windows should close automatically.
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Advanced CrossFire Searching |
The Beilstein and Gmelin databases are large
and complex; the Commander/CrossFire search system is extremely powerful
and flexible. These instructions cover only the most basic introduction
to a few of the search features available. Additional guides for fact/property
searching, reaction searching, and advanced searching tips and tricks are
available at the Chemistry
Library Beilstein information page. More information may be found in
a set of manuals produced by Beilstein Information Systems, Inc. (located
in the Chemistry Library office), as well as in the Help menus in CrossFire
itself. If further assistance is needed, contact the Chemistry
Librarian for assistance or to arrange a workshop/training session (any
level, beginner through advanced, individuals or groups). |
About the Authors |
This guide was created by Andrea Twiss-Brooks (Bibliographer for Chemical
and Geophysical Sciences) and Barbara Kern (Physical Sciences/Reference
Librarian) at the University of Chicago's John Crerar Library. Any comments,
suggestions, or corrections should be sent to Andrea Twiss-Brooks (atbrooks@midway.uchicago.edu)
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or Lasso 
tool
to highlight portions of structure