Installing Marvin

Marvin is not developed by SRI International, and is not included in the Pathway Tools distribution. Marvin must be obtained from ChemAxon and then installed. Obtaining and using Marvin is free of charge for most types of users, although it is a commercial product. Marvin is updated continuously, and new versions become available routinely. The ChemAxon web site does offer the older versions, so if the most recent version proves incompatible, download an older version. Version 4.0.3 is known to work with Pathway Tools 10.5.

Downloading

Download Marvin from the ChemAxon web site (http://www.chemaxon.com/marvin/). Note that Marvin is offered in two packages: Marvin Beans (applications for end users and Java Classes for developers) and Marvin Applets (Java Applets for web developers). The latter package, which is the one needed for Pathway Tools integration, can be downloaded from http://www.chemaxon.com/marvin/do-download-marvinapplets.html The Marvin Applets are also available in two packages: a Marvin binaries package, which includes only binary files, and a Marvin all package, which includes the signed and unsigned applets as well as examples, documentation, and sources for molfile compression. You should download the Marvin all package.

The Marvin all package is available in both tar.gz and zip formats. For Windows you would typically want the zip file, which will look like marvin-all-4_1_5.zip and for UNIX you would want marvin-all-4_1_5.tar.gz (notice that the version number will probably be higher).

Installation in UNIX

On UNIX platforms, uncompress the file that you downloaded using the command 
unzip marvin-all-4_1_5.zip
or 
tar zxvf marvin-all-4_1_5.tar.gz
Next, define a shell environment variable called MARVIN_PATH and set it to the path of the jmarvin.jar file. It is best to do this in one of the user's shell init scripts such as .cshrc or .login. For example, in csh syntax: 
setenv MARVIN_PATH /example/of/full/marvin/path

Installation in MS Windows

Unzip the file you downloaded into a newly created local directory (e.g., C:\Program Files\ChemAxon\Marvin).

Next, you need to create an environment variable called MARVIN_PATH, and set it to the full directory path in which the file jmarvin.jar was installed. To do so: right-click on the "My Computer" icon (on the desktop), and choose "Properties". In the window that opens click on the "Advanced" tab, then click on the "Environment Variables" button. A window like the one depicted in the Figure below will open.

Under "System Variables" click the "New" button and type MARVIN_PATH for the Variable name, and the full path of the jmarvin.jar file for the Variable value, as seen in the Figure below.