Images of Biological Molecules
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The majority of the following files are downloaded with the name "moldraw" -
some files will be named "moldraw.html". Therefore, when the file is
retrieved, you will need to rename the file to whatever you wish, but, you MUST
use a .pdb extension in order for your PDB (Protein DataBank) viewer to load and
display them using the 3-dimensional coordinates within the file. As mentioned
below, if you do not wish to view the images in 3-dimension, most of the files
are downloadable in a static "GIF" format
The images one can retrieve from the NIH Gopher Server are
displayed only through a search - one must know the name of the protein.
And, the images are in .pdb format which requires a graphics software such as
RasMol to view (get raswin.zip
if you are using a Windows platform). RasMol may also be accessed via
The RasMol HomePage.
The NIH Molecular Modeling HomePage, National Institutes of Health Link
will access a Beta Version of the PDB Databank at Brookhaven National
Laboratories - one may choose .pdb files from the vast array of images listed
in an easy-to-use table, or, one can search for an image by accessing:
Molecules 'R Us.
Once a listing of images appears, select the image to download - a Form
will then appear with the .pdb file as the default - if a .gif is desired,
select "image-type" in the Form provided.
The images one retrieves from the Rutgers Gopher site, are also .pdb,
but these files are molecular coordinate files (download files with the .pdbs
extension, and view in RasMol).
To locate the images at the Rutgers HTTP site, access one of the
listed files, then, scroll to the bottom of the Page - there you will find the
images (Note: some of the files may not yet have a .gif format image prepared).
The RasMol HomePage at the University of Massachusetts, Amherst,
is an excellent site which has many images, links to pdb files, and links to
software to view these files.
Most of the images depicted at Brookhaven are 3-D viewable. To see the image
in 3-D, while looking at a spot directly between the two images, cross one's
eyes slightly until a third image appears between the two. Relax, and allow
your eyes to focus on this third image - it may be necessary to slowly
move your face slightly further from or slightly closer to the
monitor screen in order to see the image clearly. Keep practicing, I
promise you that you can learn to see in this way - the brain is amazing...
You may practice on this image.......
DNA
Folded Nucleotides (Nucleic Acids) .gif conversion from .pdb
(chain view in RasMol)
From Rutgers Nucleic Acid Database .pdb Cooordinate Files
at: gopher://ndbserver.rutgers.edu:70/11/etc/ndb_link_files
Whole IgG Molecule
.gif conversion from .pdb (chain view in RasMol)
From .pdb Cooordinate Files
at: http://www.umass.edu/microbio/rasmol/padlan.htm
Heavy-chains in blue, blue-green; Light-chains in green, yellow;
Carbohydrate in red
Catabolite Activator Protein
(Bacterial, in blue) - Interaction with
DNA From the Nucleic Acid Database - Rutgers
Methionine Gene Repressor Protein
(in blue) Bound to Promoter/Operator Region of DNA (multi-colored)
Met Repressor - Same as Above in Backbone/Chain View (this
time, DNA in blue)
Interleukin 1-Beta
From the Histo Site's
Logo
Major Histocompatibility Complex Class I Protein with Bound Peptide
Acetylcholine Esterase - with Acetylcholine in binding site
RasMol-modified .pdb format (chain view) to .gif to reveal Ras
protein (oncogene product) complexed with a nucleotide (in red)
And, here are some images of immune system molecules involved in cell
recognition and immune responses:
Molecules of the Immune System
Acknowledgement: My thanks to Florida's Bill
Weinkle for his introduction to RasMol, his help, and his many well-turned
phrases.
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