Molecular-Graphics Viewers and Sample Images
Further
investigation on protein structure can be done using RasMol, a free, interactive molecular-graphics viewer.
RasMol allows users to explore the three-dimensional
shapes of molecules.
To learn more about RasMol now, click here.
The following
are links to sites featuring samples of the kinds of images that can be created
using RasMol:
·
RasMol Images by Roger Sayle. Four high-resolution images
illustrating RasMol's best by the creator of RasMol.
·
RasMol Images by Eric Martz. Images from "movie"
scripts on DNA, antibody:antigen, major histocompatibility proteins presenting
peptide antigens, SH2 domain with phosphotyrosine. Also non-script images of
ATP, tRNA, and lipid bilayers.
To download Rasmol, please use the following links, depending on your operating system:
·
Unix
RasMol can
display any molecule for which a 3-dimensional structure is available.
In order to display a molecule, RasMol needs a data file called an atomic
coordinate file. This data file specifies the position of every atom in
the molecule, as cartesian coordinates X, Y, and Z. There are several
"standard" formats for atomic coordinate files. One of the most
common is the Protein Data Bank or PDB format. The PDB Lite website may be used
to search for atomic coordinate files for macromolecules of known shapes using
their English names. Alternatively, Blast searches by primary sequence against
the NRL 3D(PDB sequences) database may be conducted at the NPSA
site to obtain atomic coordinate files. This type of search returns the
closest molecules with known structures matching the one that has been
input.
Three PDB files
have been provided below to allow hands-on experimentation. You may download
each file to your hard disk and open it using RasMol. The first file is the PDB
for Biosynthetic Threonine Deaminas, which is the closest structure
matched to Mamalian Serine Racemase, available in PDB format. The second
file is the PDB for Alanine Racemase, which is the closest
structure matched to Bacterial Serine Racemase. The third file is
the PDB for DNA Polymerase I, which is the closest available PDB
file matched with L-lysine 2,3-aminomutase. You may click
the links below to download each file:
·
Biosynthetic
Threonine Deaminas
NOTE: Chime is an
alternate viewer program that provides all the functionality of RasMol but
allows you to view the molecule directly within your web browser. To learn more
about Chime and to download the Chime plug-in, click here. If you have the
Chime plug-in correctly installed, the above links will display the proteins in
this browser window itself.
RasMol and Chime allow you to explore the three-dimensional structures of proteins by moving them in all three axes while providing tools such as zooming, multiple color schemes and different visual representation styles. Still pictures such as those below can also be exported using RasMol and Chime.
