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:
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.
- 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
Here is the RasMol configuration procedure for Netscape.
(It has been tested on Netscape versions 2.01 and 3.0.)
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.)
- 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
- 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
Örjan Hansson's Molecular Visualization site at
Dept Biochemistry/Biophysics, Goteborg Univ SE, from which
parts of this page were taken.
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