Instructions for downloading PDB structural
files for viewing (Mac Users):
Many structures have been
recently resolved, and the Protein Data Bank (PDB) at the Research
Collaboratory for Structural Bioinformatics is an excellent source for these structures. These instruction will allow you to download
the PDB files onto your computer for viewing through the use of Roger Sayle’s RasMol.
1. You
can search for the desired molecule at the Protein Data Bank two different
ways. First, it you know the PDB
Identification number enter it into the box on the right side of the page that
says PDB I.D. To do a key word search
mouse click on “Search Lite” which provides a simple keyword search.
2. A list of molecules will be returned, in
order of relevance. A brief description
will accompany each of the returned selections. From this you should be able to identify whether the structure is
that which you are searching for. Play
close attention to the type of molecule (ie. binding, transferase, chaperone …). Also pay attention to the resolution, which gives an idea on the
quality of the picture (resolution is denoted by a distance in angstroms, the
smaller the better the resolution).
3. To select a certain molecule for further
investigation, mouse click on the red Explore icon that is on the right
of each returned entry. This will show
the summary information.
4. We are specifically interested in the
structural information, so mouse click on View Structure that can be
found on the left portion of the screen.
This will give a variety of versions of the structure.
5. We will be using the RasMol program. Mouse
click on the Rasmol hot link. If
you are immediately prompted to save the file to your desktop, do so and the
file is now ready to be viewed. However,
if the file is not immediately saved continue to direction 6.
6. If a window opens with structural information
go to the main command line and select File => Save As, and save the
file to your desktop.
Viewing a Saved Structure:
7. Open the RasMol program by mouse clicking the
program. If it does not appear on the
screen go to the main command line and select Window=>Main Window and
do this again but select Window => Command Line.
8. Select File => Open and select the
structural file (ending in .pdb) that you wish to view. If the structural files do not appear on the
desktop or in the file that you put them in, you can use the Rasmol load
command in the command line (which has a white background and may be hiding
behind the black viewing window). In
the command line type load filename.pdb, (ie load 1hho.pdb). These files will not be found unless they
are saved on your computer. Be careful
not to confuse the number “0” with the letter “O” which often look similar in
pdb file names.
When you are
ready to proceed to the Protein Data
Bank at the Research Collaboratory for
Structural Bioinformatics select the following link:
You may also try to search
for your protein structure in NCBI’s Entrez Structure Search. Each structural protein on
file in the NCBI Database has a direct link to the corresponding PDB structure
file. Then you can proceed to download the file from PDB.