Revised 8/21/98
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.
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.