Configuring Netscape

Configuring Netscape      For Using Molecular Viewing Programs
Contents RasMol    Other Modeling Programs      Configuring
Follow these instructions if you want Netscape automatically to open atomic coordinate files with your favorite molecular viewer whenever you download such files from the Protein Data Bank, this website, or other sources.
RasMol
   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 95 USERS: The desktop copy of RasMol cannot be a shortcut (what Mac and UNIX calls an alias). It must be a true copy of the program. On a Windows 95 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.
Other Modeling Programs
   If you are configuring Netscape to use SwissPdbViewer or any modeling program other than RasMol as a helper, you can run the modeling program from its own folder on your hard drive.
Configuring
   Netscape uses MIME types in order to know which helper application to use in opening the 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.
Instructions for Netscape Communicator 4.0.4 (for Navigator 3.0.1, see below)
Set the desired modeling program 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. The Edit Type form appears. Fill it out as follows:
Description: chemical/x-pdb
MIME type: chemical/x-pdb
Suffixes: pdb
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)
6) button: OK (closes the Edit Type form, returns you to Preferences window)
If you plan to view RasMol scripts (like those provided for CHY361), 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 a file from the Protein Data Bank by way of the link RasMol Asymmetric Unit, your browser should automatically start your modeling program (RasMol or other) and open the file. Some files of type chemical/x-pdb will appear on your desktop with the name send-ras or send-ras-# (a random number). Immediately rename the file #xxx.pdb, where #xxx is the four- character file code for the PDB file. This file code is given on the PDB page from which you obtain the file, and is also given in the file.
     Press the Back button on your web browser to return to the previous page.
Instructions for Netscape Navigator 3.0.1
Set the desired modeling program as the helper application for files of MIME type chemical-x/pdb, as follows):
1) Options: General Preferences
2) Click the file-folder tab labeled Helpers. Then look down the Description 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. The Edit Type form appears. Fill it out as follows:
Description: chemical/x-pdb
MIME type: chemical/x-pdb
Suffixes: pdb
3) In the area labeled Handled By, click to mark the button Application.
4) button: Browse ...
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)
6) button: OK (closes the Edit Type form)
7) button: Apply (on the General Preferences window)
   If you plan to view RasMol scripts (like those provided for CHY361), follow the same procedure (steps 2-7) to set RasMol as the helper application for files of MIME types application/x-spt and application/x-rasmol.
8) button: OK (closes the General Preferences window)
Now when you download a file from the Protein Data Bank by way of the link RasMolAsymmetricUnit, your browser should automatically start your modeling program (RasMol or other) and open the file. Some files of type chemical/x-pdb will appear on your desktop with the name send-ras or send-ras-# (a random number). Immediately rename the file #xxx.pdb, where #xxx is the four- character file code for the PDB file. This file code is given on the PDB page from which you obtain the file, and is also given in the file.
Press the Back button on your web browser to return to the previous page.