4MRNA

4MRNA is an abbreviation for “Massive Multi-type Model Molecular Replacement for Nucleic Acids”. 

This is a novel method designed to enhance molecular replacement for phasing in X-ray crystallography of nucleic acids. 

For more details, please see the “About” section. 

Before using 4MRNA, please complete a simple installation procedure. The software also depends on the external programs 3DNA and Phaser, which must be installed beforehand. These installations are required only once before using the software for the first time. 

The installation procedure is described in the “Download” section.

To run 4MRNA, simply type 4MRNA in the command line. After answering a few initial questions, you only need to wait for the process to finish. Once it is completed, you can proceed to structure refinement using your preferred method.

In addition, an advanced execution mode for expert users is also available. 

For detailed procedures, please refer to the “Instruction” section.

If you use 4MRNA in your research, please cite the following reference. In addition, please also cite the external software packages used by 4MRNA.

• 4MRNA: The manuscript describing 4MRNA is currently in preparation. Until it becomes available, please cite the following GitHub repository: https://github.com/S-Ando-Biophysics/4MRNA.

• 3DNA: Lu, X. J., & Olson, W. K. (2008). 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nature protocols, 3(7), 1213–1227. https://doi.org/10.1038/nprot.2008.104 

• Phenix: Liebschner, D., Afonine, P. V., Baker, M. L., Bunkóczi, G., Chen, V. B., Croll, T. I., Hintze, B., Hung, L. W., Jain, S., McCoy, A. J., Moriarty, N. W., Oeffner, R. D., Poon, B. K., Prisant, M. G., Read, R. J., Richardson, J. S., Richardson, D. C., Sammito, M. D., Sobolev, O. V., Stockwell, D. H., … Adams, P. D. (2019). Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta crystallographica. Section D, Structural biology, 75(Pt 10), 861–877. https://doi.org/10.1107/S2059798319011471 

• Phaser: McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007). Phaser crystallographic software. Journal of applied crystallography, 40(Pt 4), 658–674. https://doi.org/10.1107/S0021889807021206