Command Line Arguments

Specifying an Input File
Configuring Web Browsers to Invoke Fungimol

Specifying an Input File

Fungimol can take zero or one command line arguments. If the command line argument is specified, it is interpreted as the name of an input file to read. For example, if you have installed Fungimol in the standard place and you give the command

fungimol /usr/doc/fungimol-FUNGIMOL_VERSION/tutorial/molecule/benzene.pdb

you'll see a benzene molecule.

Configuring Web Browsers to Invoke Fungimol

Because Fungimol takes an input file as a command line argument, it is possible to configure web browsers to use Fungimol as a viewer for pdb files or any other file format that Fungimol can read. For Netscape 4.72, the procedure for doing this is:

Select "Edit" from the menu bar at the top.
Select "Preferences..." from the pulldown menu.
Select the rightward-pointing triangle to the left of the word "Navigator".
Select "Applications".
If there is an entry with the description "PDB files" or something synonymous, click on it and select "Edit...". Otherwise select "New...".
Update the form to have these values:

Field Value

Description PDB files

MIMEType chemical/x-pdb

Suffixes pdb

Application xterm -e /usr/bin/fungimol %s
Make sure the radio button next to "Application" is selected.
Select "OK" and then "OK" again.

Field	Value
Description	PDB files
MIMEType	chemical/x-pdb
Suffixes	pdb
Application	xterm -e /usr/bin/fungimol %s

Now you can browse the web looking for PDB files to read. For example, Fungimol works reliably with the differential gear at http://www.imm.org/Parts/Parts3.html.

Command Line Arguments

Contents

Specifying an Input File

Configuring Web Browsers to Invoke Fungimol