Java, already installed.

Here is the procedure to install Jmol:

• Jmol is distributed as a JAR archive, ready to execute through a startup script. Create a folder under /home/bioubuntu to put all this and move this folder into /opt/bio/sources.

• This shoulder should belong to root and its permissions set to 755.

% sudo chown -R root:root /opt/bio/sources/jmol-11.7.46
% sudo chmod 755 /opt/bio/sources/jmol-11.7.46

• Once you are in /opt/bio/sources/jmol-11.7.46, the jmol script needs to be edited to add a JMOL_HOME bash environment variable. At the very top, just under the #!/bin/sh line, add this line:

export JMOL_HOME=/opt/bio/sources/jmol-11.7.46

• To make sure that jmol is available to all, do this:

% sudo ln -s /opt/bio/sources/jmol-11.7.46/jmol /usr/local/bin/jmol

• To add Jmol to the Impilo application menu, you need to edit the Xfce4 configuration file:

% sudo xfce4-menueditor /etc/xdg/xfce4/desktop/menu.xml

• The three items to add are:
  • Item: Launcher
  • Name: Jmol
  • Command: jmol