Follow these instructions if you want Netscape to open atomic coordinate files automatically with your favorite molecular viewer whenever you download such files from the Protein Data Bank, this website, or other sources.
If you are configuring Netscape to use Deep View (SwissPdbViewer or any modeling program other than RasMol as a helper, the modeling program can reside in any folder or directory on your hard drive.
Deep View (Swiss-PdbViewer)
Users (including CHY 361 students):
Skip to Configuring.
RasMol has several unfortunate quirks that can be evaded if RasMol is present on the desktop, and already running, before Netscape downloads a file for viewing in RasMol. If you are configuring Netscape to use RasMol as a helper, make copies of the RasMol program and its help file rasmol.hlp on your desktop by holding down the option key, dragging their icons out of the RasMol folder, and releasing them on the desktop.
NOTE TO WINDOWS USERS: The desktop copy of RasMol cannot be a shortcut (what Mac and UNIX call an alias). It must be a true copy of the program. On a Windows computer, it is also recommended that the desktop copy be the only copy on your hard drive.)
Before you download a file for viewing in RasMol, start RasMol by double clicking on this desktop copy of the program. This assures that when Netscape runs RasMol, the desktop copy is the one that runs.
This procedure is critical if you plan to download and run RasMol scripts, because most scripts start by loading a PDB file, which must be in the same location as the script and the running version of RasMol. This arrangement is also convenient if you write your own scripts, because they will automatically be saved to your desktop.
Netscape uses MIME types in order to know which helper application to use in opening a file. Atomic coordinates files come from the Protein Data Bank (and this website) with MIME type chemical-x/pdb. You must tell Netscape to use your desired modeling program to open files of this type.
Follow these instructions if your viewing program is Swiss-PdbViewer (Deep View), or any program other than RasMol.
Set your desired modeling program (such as Swiss-PdbViewer) as the helper application for files of MIME type chemical-x/pdb, as follows:
1) Select Edit: Preferences
2) On the Preferences window, click on Category: Navigator: Applications
Under Description, look down the list for chemical/x-pdb. If you find it, click to select it, and then click Edit. If you do not find it, click New. Either way, the Edit Type form appears. Fill it out or correct it as follows:
Description: chemical/x-pdbMIME type: chemical/x-pdb
Suffixes: pdb, pdb.gz
3) In the area below the list, click to mark the button Application.
4) button: Choose ...
Navigate to the folder that contains the modeling program (to the
desktop if it is RasMol). Click once on the program name to select
it.
5) button: Open (this action should close the top dialog box)
Repeat steps 2-5 to set your desired program as the helper application for binary executables (MIME type "application/octet-stream"), specifying the file type as "text" in the bottom section of the dialog. If you sometimes download other types of binary executables, complete this task by setting the dialog to save the downloaded file to disk.
6) button: OK (closes the Edit Type form, returns you to Preferences window). You should now see that files of type chemical/x-pdb will be handled by the modeling program you selected.
(RasMol ONLY: If you plan to view RasMol scripts, follow the same procedure (steps 2-6) to set RasMol as the helper application for files of MIME types application/x-spt and application/x-rasmol.)
7) Click OK to close the Preferences window.
Now when you download an uncompressed file in PDB format from the Protein Data Bank, your browser should automatically start your modeling program (Deep View or other) and open the file.
If you can download PDB files, but your modeling program does not start automatically, start the modeling program and use its File: Open command to open the file. This is called "opening the file within the program".
If this situation persists, go back to step 2 and specify "Save to disk" on the Edit Type form. Then you will always get a Save dialog when you download PDB files. With the Save dialog, you can direct the file to a convenient location and open it within your modeling program.
Close this window to return to the SPdbV Tutorial. Press the Back button on your web browser to return to other pages.
NOTE: If you use Microsoft Internet Explorer and would like to provide instructions for this configuration on that browser, please send me your instructions and I will post them here.