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Nmrglue: an open source Python package for the analysis of multidimensional NMR data

Journal of Biomolecular NMR volume 55, pages 355–367 (2013)Cite this article

Abstract

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

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Acknowledgments

This work was supported in part by the National Science Foundation (CAREER Award MCB-0745754 to C.P.J.), the National Institutes of Health (R01GM094357 to C.P.J.), the Camille and Henry Dreyfus Foundation (Camille Dreyfus Teacher-Scholar Award to C.P.J.) and Eli Lilly and Company (Young Investigator Award to C.P.J.). The authors thank the current and former members of the Jaroniec research group (in particular P.S. Nadaud, M. Gao, C. Gupta, S.P. Pondaven, I. Sengupta, B. Wu and S. Mukherjee) for testing and providing valuable feedback on the early versions of nmrglue, and M. Fenwick and P. Semanchuk for reporting bugs and providing patches for the package. This work would not have been possible without the Scientific Python community, whose efforts have produced a powerful environment for scientific computing. The members of this community are too numerous to list here, however special thanks go to the late J.D. Hunter for his dedication to the community and contributions to creating the indispensable matplotlib package. J.J.H. also thanks J. Hoch (U. Connecticut Health Center) for supporting his continuing work on the development of nmrglue.

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  1. Jonathan J. Helmus

    Present address: Environmental Science Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL, 60439, USA

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA

    Jonathan J. Helmus & Christopher P. Jaroniec

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  1. Jonathan J. Helmus
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Correspondence to Jonathan J. Helmus or Christopher P. Jaroniec.

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Helmus, J.J., Jaroniec, C.P. Nmrglue: an open source Python package for the analysis of multidimensional NMR data. J Biomol NMR 55, 355–367 (2013). https://doi.org/10.1007/s10858-013-9718-x

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Keywords

  • Nuclear magnetic resonance
  • Solid-state NMR
  • Data processing
  • Data analysis
  • Data visualization
  • Python
  • Open source