Getting PDB Files Revised 8/21/98
Contents
Notes
Getting the File
Notes
It is a good idea to configure
Netscape to open PDB files with the modeling program of your choice. See Configuring Netscape.
You need to know the PDB code for the file you wish to obtain (but see Note below for access to searching). The code consists of four
characters, the first one a number; for example, 1hew is the code for a file
containing the atomic coordinates of lysozyme. In the following instructions, the code is
listed as #xxx.
Getting the File
The first menu command below
opens a new window in Netscape. Use the window in which you are now reading to continue
reading instructions. Use the new window to carry out the commands. Bring either window to
the front by clicking any part of it.
If there are alternative commands, the first is for Netscape
Communicator 4.0.4 and the second is for Netscape Navigator 3.0.1.
File: New: Navigator Window or File: New Web Browser
In the new window, direct the web browser to the Protein Data Bank, as follows:
File: Open: Location in Navigator or File: Open Location
Type http://www.pdb.bnl.gov/ in the space
provided (recent versions of browsers do not require the initial http://www).
button: Open
You should see the home page of the Protein Data Bank at Brookhaven National
Laboratory.
link: 3DB Browser
On the 3DB Browser form, click to place a cursor within the box marked PDB ID Code,
and type #xxx (the file code for the PDB file you want).
Note: before
proceeding, look over the form. Notice that you can search the entire Protein Data Bank
just like searching in the library. The 3DB Browser is a powerful tool for finding
protein structures that are of interest to you, even if you do not know a specific PDB
code name. Read the form to find links to further instructions for searching the PDB.
button: Search
The search produces a 3DB Atlas entry for #xxx. From this entry, you can follow links
to many sources of information about this molecule.
link: [Save to Disk] (under Data Retrieval)
You will get a Netscape message asking what to do with the file. Simplest is to click
"Save File" and direct the file to a convenient location like the Desktop. Later
you can view it with the graphics program of your choice, or read it in a word processor.
During a download, if Netscape simply displays the contents of the file in a
Netscape window, save the file to the desktop as a text file, with the name #xxx.pdb.
Then open it in your modeling program.
To read about the model you are retrieving,
link: [header only] (under Data Retrieval)
You will see the header (comments) for the PDB file, which begin with
citations of papers published about this substance. In most cases, the citations contain
links to abstracts of the papers, which give you the main conclusions drawn from the
structure. These abstracts are in Medline, which provides links to related articles, as
well as tools for further searching. Because of these links, it is to your advantage to
read the file header online.
Close this window to return to the SPdbV Tutorial. Press the Back
button on your web browser to return to other pages.