Searching the Chemical Literature by Computer at Stony Brook
Searching the Cambridge Structural Database Via Conquest
The Cambridge Structural Database contains information on the crystal structures
of more than 240,000 small molecules. This Database can be accessed from the computers
in the Chemistry Library and in the Chemistry SINC Center on the fourth floor
of the Graduate Chemistry building and the Chemistry Graduate Student SINC site
on the third floor of the Graduate Chemistry Building. On these computers you
run the Program Conquest. The help files in Conquest are particularly useful.
Stony Brook currently has a site license for Conquest such that it can be installed
on any PC or Unix computer: see the chemistry librarian, April
Brazill or Steve Koch.
More complete help files are available:
CSD Help Files
Some short notes for Searching for Organometallic
Pi System in the CSD and Crossfire Gmelin
Exporting Coordinates from Conquest to other Graphics Programs.
In Conquest, it is possible to save the 3D Visualiser view of a molecule as a
JPEG image. However it is better to export the Coordinates of a molecule from
Conquest into Professor Joe Lauher's Molecular Graphics program, Chem-Ray:
In Conquest export the coordinates of a particular stucture (using the COORD:CSE
coordinate file format) and open them in Chem-Ray (using the *.cor). Similar
procedures can be used to export coordinates of molecules into other programs.
Visualizing Molecules Using Chem-Ray
Professor Joe Lauher's Molecular Graphics program, Chem-Ray, is installed
on the chemistry SINC center computers on the Fourth Floor and in the Chemistry
Library. It is also installed on the computers in the Graduate Student SINC
site. Some instructions on using Chem-Ray
are given here. To get started open the basic.ctb file using the file (then
open) pull down menus. Read the mouse commands for rotating the molecule and
resizing the graphic windows. Explore the different dynamic styles. Use the
arrow button on the top right to cycle through the different molecules.
Protein Data Bank
The PDB
contains the information and coordinates for Proteins whose structures have
been determined by X-ray crystallography or NMR techniques. There are currently
more than 16,500 structures in the PDB. The structures can be visualized by
a number of different graphics programs. A convenient (and free) methods uses
Netscape (version 4.7 but not Version 6) and the Chime
plug-in. (Using Microsoft's Internet Explorer with Chime is frequently problematic).
Here are some simple instruction on using Chime
to display a protein structure
Getting Started: Search for the protein you are interested in. Chose
the particular protein by clicking on explore (on the right). Chose View Structure
on the Left Menu. Chose option Protein Explorer.
You can read about Protein
Explorer here.
There are many useful Biochemistry Tutorials on the structures of proteins
and DNA at: World Index
of Molecular Visualization Resources
Crossfire Beilstein and Crossfire Gmelin
Crossfire Beilstein and Gmelin are powerful databases to the properties of organic
and inorganic compounds respectively. Access to these databases are available
on the computers in the Chemistry library and on the fourth floor SINC center
and in the Graduate SINC site on the third floor. Access can also be obtained
on any PC or Mac computer which has a sunysb.edu IP address using client software
that can be downloaded from www.library.wisc.edu:4001/
(See the chemistry librarian, April
Brazill, for the necessary password).
Instructions on using Crossfire can be obtained from a series of manuals which
are on reserve in the Chemistry Library (the tutorials to Crossfire Beilstein
and Crossfire Gmelin are recommended). There is a short manual which can also
be downloaded at http://www.beilstein.com/data/xfstrt2000.pdf
There are also a number of Web sites that are very useful
www.lib.uchicago.edu/~atbrooks/beilfact.html
www.library.wisc.edu/libraries/Steenbock/beilstein/home.htm
www.beilstein.com/products/xfire/
SciFinder Scholar
Scifinder Scholar enables computer searching of Chemical Abstract including the
ability to do substructure searching. Currently only five people in the university
can use Scifinder at any one time; so be sure to log off from Scifinder when you
are finished using it. SciFinder Scholar requires a client software program to
be installed on a PC or a Mac computer. SciFinder can be installed and used on
any computer that has a Stony Brook IP address. The program is available for downloading
by Stony Brook staff and students at SciFinder
installation. There are some instructions for using SciFinder Scholar at http://www.cas.org/SCIFINDER/SCHOLAR/resources.html.
Web of Science
The Web of Science enables searching
of the entire scientific literature via the WWW web. A key feature is the Science
Citation Index by which the literature citation of a published paper can be obtained.
The Web of Science is available 24 hours a day by up to 15 Stony Brook users.