Home

MOLMOL DESCRIPTION

MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.

MOLMOL ENHANCEMENT PROJECT 2013

The project's vision is to enhance the longevity of the MOLMOL application and promote its ongoing use in the NMR (nuclear magnetic resonance) research community.

To facilitate this vision one of this project’s major goals is to implement a more structured and open source based methodology for the application using SourceForge web services. This will facilitate ongoing maintenance, support and the development of new application features. This will also provide version control for the MOLMOL application source code and simplify the distribution and access to platform specific application binaries. Another major goal of the project will be the implementation of long awaited fixes to existing software errors and enhancements to address existing software deficiencies.

This project is aimed specifically at taking the MOLMOL 2K.2 custom version derived from MOLMOL 2.6 by Reto Koradi and placing this in SourceForge.

This strategy is being driven by a software project originating from the James Cook University in Australia but the long term vision is to utilise the resources and good will of the open source community.

TRIGGERING PROBLEMS/OPPORTUNITIES

The MOLMOL application was last maintained in 2003 and consequently over the last 10 years there has developed a need to rectify identified bugs in the software as well as a need to enhance existing features and develop new features in the application. This would add to the existing and recognised usefulness of the MOLMOL application to the NMR community and consequently promote its continued use in this important field of research.

A related but more critical operational issue occurred recently(2013) when a new version of the Mac platform was released and the MOLMOL application code not be recompiled and executed in this new environment. This highlighted the fact that there was no expertise readily available which could address this ongoing issue and more importantly the fact that the MOLMOL application build process was essentially unknown. The project clients who are leaders in the NMR field have advised that this is an ongoing issue.

The current(2013) literature describes the MOLMOL application as “abandonware” and given the issues above this description appears to be appropriate. The development work planned and implemented by the successful completion of this project will address many of the significant issues and deficiencies that have been found in the MOLMOL application since it was last maintained in 2003.

By bringing the current MOLMOL application into an open source based development and support environment this would capture the existing application as it currently stands and enable the ongoing maintenance and enhancement of the application by the large open source community. This environment would also facilitate the refactoring of code and reengineering of the MOLMOL application in a source code version controlled environment which when correctly applied typically leads to a much better software product. Furthermore this type of open source environment also facilitates the distribution of platform specific binaries which simplifies the end user application installation experience and process.

RECOGNITION OF ORIGINAL AUTHORS

It must be noted and recognised that the original MOLMOL software was developed by Reto Koradi, Martin Billeter and Kurt Wüthrich in 1996. When plots prepared by MOLMOL are used in lectures, publications or other similar occasions, then a reference to the authors and the following paper is to be made:

Koradi, R., Billeter, M., and Wüthrich, K. (1996)
J Mol Graphics, 14, 51-55.
MOLMOL: A program for display and analysis of macromolecular structures.

INSTALLATION

See the installation wiki page for details on how to access the MOLMOL application.

MANUAL

See the manual wiki page for details on how to use the MOLMOL application and useful beginner tutorials.

RESOURCES

See the resources wiki page for useful web resources.

DEVELOPERS

Details regarding how to access the source code and compile the MolMol application can be found here on the developers wiki page.

BETA TESTING 2013

Currently Beta testing has been started for the "MOLMOL Enhancement Project 2013" and the procedure can be found here on the beta testing wiki page.