MarvinSketch

The Marvin Suite is a free software package produced by ChemAxon. Its primary uses are drawing chemical diagrams with MarvinSketch, visualizing 2D and 3D structures with MarvinView and MarvinSpace (respectively), and converting structure files with the utility MolConverter.

The Marvin Suite also comes with a proprietary set of calculator plugins that may be useful to users. The copy of Marvin Suite installed on the CHPC systems allows limited use of these plugins. However, users may obtain free single-user academic research licenses which will provide full access to these plugins and other ChemAxon software packages. Details on using this license on CHPC systems will follow.

Using MarvinSuite

In order to access MarvinSuite, source the setup files using the appropriate shell extension (or add a line to your .aliases). The current version is 6.1.2 for RHEL6.

source /uufs/chpc.utah.edu/sys/pkg/marvin/std_rh6/etc/marvin.{sh,csh}

Note that there is a separate version for RHEL5 (sanddunearch, updraft). In that case, replace std_rh6 with std. Once sourced, the user can access the software with any of the following commands (case sensitive):

MarvinSketch
MarvinView
MarvinSpace

Obtaining and installing a ChemAxon license

Obtaining a license will require obtaining a free account from ChemAxon, found on their registration page. Once you have an account, you can request an personal academic license here. The license is good for two years (as of Nov 2013) from the time of approval and can be used with any of their software. The license can be renewed after two years if ChemAxon if the software is used for and cited appropriately in a journal publication. Also, please note the specific stipulations of the license and academic research uses. For questions on licensing, please contact ChemAxon.

The license will be emailed to the user after approval. ChemAxon has authorized CHPC to allow users to place personal licenses on their home directories.The user will need to make a new directory and chmod it so that only the users has access:

mkdir $HOME/.chemaxon
chmod go-a $HOME/.chemaxon

The user can then copy the license file to the folder and gain access to any ChemAxon software, particularly the calculator plugins for the Marvin Suite. It is up to the user For additional help, please contact the CHPC helpdesk at issues@chpc.utah.edu.