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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
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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