Starting Your Downloaded Copy of Protein Explorer (PE)

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I. Choose a compatible browser.

Here is a list of compatible browsers (all free) and where to download them.

Windows: see list at the above link.

Intel Mac OSX: Use MS Windows (supported, for example, by

PPC Mac OSX: You must have Classic (OS9) to use PE. PE requires the Classic application Netscape Communicator 4.x (4.8 is recommended; downloading instructions). (No other browser works. Netscape 7 and 8 do not work.)

ALL PLATFORMS: If you're not sure whether your browser is compatible, go ahead and try starting PE -- if you need a different browser or version, PE will explain how to proceed. If you have already installed Netscape 7 or 8 and like it, it is perfectly OK to install Netscape 4.8 in addition (just be sure to specify a separate directory location). When installed in separate locations, the two versions will not interfere with each other.

Appearance of Protein Explorer after clicking Quick-Start in a compatible browser.
II. Verify browser compatibility.

Before you attempt to run your downloaded copy of Protein Explorer (PE), make sure you can run Protein Explorer on-line from At the FrontDoor there, click the large Quick-Start link in the yellow box near the top. If your browser is compatible, you will soon see the PE's FirstView of 1d66, as shown on the right.

If your browser is not compatible, attempting to start PE will automatically tell you how make it compatible. It is best to get this resolved before attempting to run your downloaded copy.

Seeing the 1d66 molecule (yeast Gal4 complexed to DNA) in PE, as shown on the right, verifies that your browser is compatible. After you have seen the molecule from PE running on-line, proceed to start your downloaded copy as explained below. If you think you have a compatible browser but PE never displays the molecule, see troubleshooting.

(If you do not have an Internet connection, go ahead and start your downloaded copy as explained below.)

III. Start your Downloaded PE!

Generally, to see a molecule in PE, you must

There are a variety of ways to specify the molecule. After you start PE, you will see them explained on the FrontDoor of PE.

Several methods you might reasonably expect to work will not work, such as double-clicking on a PDB file, or dragging a PDB file and dropping it on a shortcut/alias to PE.

Here are several alternative methods for starting PE. They are equally good -- use whichever is easiest for you.