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Documentation for installing license files issued for versions prior to 5.0 can be found here.

The possible ways of installing licenses on a server (web applications e.g. JSP pages, Pipeline Pilot):

1. Using system variables (recommended):
The location of the license file can be set with:
From version 5.3.2 it is possible to define multiple license files of arbitrary locations. The separator character is ";".
In case license files are set this way, the license files will be read from all locations defined by the environment variable, the Java system property and from the user's home directory.
Example: -Dchemaxon.license.url="C:\ChemAxon\license2009.cxl;C:\ChemAxon\license2010.cxl"
2. Automatic install:
The license file is automatically recognized when stored in the .chemaxon (Unix) or chemaxon (Windows) sub-directory under the home directory of the user running the application. The following locations are accepted:
• (.)chemaxon/license.cxl (file name is fixed)
• (.)chemaxon/licenses/*.cxl (from version 5.3.2 only - the license file can have arbitrary name, the extension is fixed)
3. Command line install:
Launch the license shell script (Unix) or license.bat batch file (Windows) available in the Marvin Beans and JChem downloadable packages.
Type license -h for the list of available options.
4. Using Java API:
chemaxon.license.LicenseManager.setLicenseFile(String path)
chemaxon.license.LicenseManager.setLicense(String s)

If the licenses are installed later, when a web application is already running, it is not necessary to restart the web server (e.g. Tomcat), the License Manager will automatically and repeatedly check if a license file was installed in the meanwhile.  Please note that Marvin JS license installation is different, the installation guide will be sent to you together with the license.

In some cases it can happen if a ChemAxon product is run as a service by the System Profile, than despite all effort no Environment Variable is visible for the product. In this case our license check falls back to search the license in C:\Windows\System32\config\systemprofile\chemaxon\ folder, which is the user home of the System Profile. I this folder you can place a license.cxl file or create a licenses folder and copy all your .cxl files here, as described in the 2. point above.