If you can't see the 3-D rotating DNA molecule below,
follow this link to download the CHIME plug-in:
Once you have installed the CHIME plug-in, you will be able to view and
manipulate the image above. Use the right mouse button (for Mac, hold the
button down) to reveal a menu that allows control of how the molecule is
displayed. The type of model can be selected under DISPLAY. Wireframe,
ball and stick, and space-filling are among the options. The COLOR
options allow the use of color to identify various parts of the molecular
structure. Selecting CPK gives a different color to each element. For
proteins, DNA and other complicated atoms, selecting GROUP will represent each
sub-unit, such as an amino acid or base, with a different color, and selecting
CHAIN will give a different color to each chain. Within the OPTIONS menu
are selections such as SPECULAR and SHADOW that can be used to make the
image look more three-dimensional. For molecules having a chiral
center, the STEREO selection displays stereoisomers side-by-side.
Holding down the left mouse button (for Mac, hold the button down while
immediately moving the pointer) allows you to change the
orientation of the molecule with respect to the axis about which it is
rotating. The ROTATION selection on the menu allows the rotation to be
turned on and off.
The image is inserted into an HTML document via an EMBED tag which points
to a source that is a .pdb file. Such files are actually text files that
contain the coordinates of each atom present along with the the links
(bonds) between them. The software generates the image from this
information. Thus, even a large, complicated molecule will have a very
small .pdb file. The attributes of the EMBED tag are used to determine the
various options for DISPLAY, COLOR, ROTATION, etc. when the page is
loaded. Once the page is loaded these options can then be changed by
the user by using the menus as described above. Please note that using
.pdb files in your web pages requires that the server on which they are
located be configured to support the MIME type "chemical/x-pdb" for files
with extension "pdb."
Also available is a stand-alone program called RASMOL that can be used for
viewing and manipulating molecules saved as .pdb files. RASMOL has
additional advanced features not available in the CHIME plug-in, including
scripting (perhaps for creating animations) and the ability to save any
view of the molecule in a variety of graphics formats such as .gif, etc.
Like CHIME, RASMOL can be downloaded for free.
For additional information about CHIME, RASMOL, and other file formats
used for molecular modeling--as well as for collections of .pdb files to
view and/or download--please see the links below.
