Configuring Netscape 2 or 3 for RasMol

This procedure configures Netscape so that when you click on a link to a PDB (atomic coordinate) file whose name ends in .pdb or .ent, RasMol will be started automatically, and will automatically load and display the PDB file immediately after it is transferred across the network.

After you have displayed the molecule in RasMol by this method, should you decide you want to save a local copy of the PDB file, you have two choices:

Best method: in Netscape, on the link to the PDB file, hold down Shift (in Windows, or Control and Alt on the Macintosh) while clicking. This forces a Save As operation instead of starting RasMol. The resulting saved PDB file will have the complete contents of the original.
Alternate method (not recommended): while in RasMol displaying the molecule, type the command "write pdb [filename]". This method saves only the atomic coordinates, losing nearly all other information in the PDB file, including the references to the published structural work. (Chime does not lose anything.)

If you have previously installed MDLI ChemScape Chime (a Netscape Plugin), you will be unable to invoke RasMol on pdb files -- Chime will be invoked instead. If you want to invoke RasMol instead (as a helper/viewer application, not a plugin, meaning it will come up in a separate window instead of appearing on the web page), you must disable Chime. Here are instructions for disabling chime. Alternatively, you could have two separate installations of Netscape (in two separate directories/folders), one with Chime installed, and one configured for RasMol.

Here is the RasMol configuration procedure for Netscape.
(It has been tested on Netscape versions 2.01 and 3.0.)

Select the Netscape menu Options/General Preferences... and the Helpers tab. Look carefully through the list. If there is already a chemical/x-pdb entry with the action "Ask User", highlight that and proceed to step 5 below. Otherwise, continue with step 2.

Click the Create New Type button.

Enter chemical in the Mime Type field, and x-pdb in the Mime SubType field.

Press OK.

Enter pdb,ent in the File Extensions field.

Mark Launch the Application: and press the Browse... button.

Select the appropriate version of RasMol on your hard disk (e.g. RASWIN.EXE) and press OK.

Press OK at the bottom of the Helpers dialog.

If all is OK you should be able to start RasMol and view Crambin from the file 1crn.pdb or from the file pdb1crn.ent. To see the contents of this PDB file, click on this copy renamed 1crn-pdb.htm.

Note: if you want to use the Brookhaven PDB's RasMol Asymmetric unit button for direct viewing (without saving to disk first) you'll need to repeat the above procedure to install application/x-rasmol. (Not chemical/x-rasmol! No file extensions need be specified.)

Thanks to Örjan Hansson's Molecular Visualization site at Dept Biochemistry/Biophysics, Goteborg Univ SE, from which parts of this page were taken.

This page maintained by Eric Martz.