Welcome to PyBMRB 1

A Python module for visualizing Nuclear Magnetic Resonance(NMR) chemical shift data from Biological Magnetic Resonance data Bank 2 (BMRB) and from NMR-STAR 3 format files. PyBMRB helps the user to view the one dimensional chemical shift list a multi-dimensional NMR spectrum. In addition to that Chemical shift distribution of different atom types can also be visualized as histograms and heatmaps using this library.

This package uses PyNMRSTAR to parse the NMR-STAR files and BMRB-API to fetch the data directly from BMRB, which avoids the hustle of downloading and parsing the data from BMRB for visualization purpose. This package is developed and maintained by BMRB.

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Sample visualizations

Click the figure caption for interactive visualization

Figure 1 : ¹ H - ¹⁵ N -HSQC

Figure 2 : ¹ H - ¹³ C -HSQC

Figure 3 : CB-Histogram

Figure 4 : Chemical shift correlation of CYS N and CB

Contents:

• Introduction to PyBMRB
  • Biological Magnetic Resonance data Bank (BMRB)
  • NMR-STAR
  • Why do we need PyBMRB?
  • How does it work?
• PyBMRB quick start
  • Installation
  • Input
  • Quick start
• Examples
  • Spectra simulation
  • Chemical shift Histograms
  • Data manipulation
• Module documentation
  • Spectra
  • Histogram
  • ChemicalShift
  • ChemicalShiftStatistics
• Release notes
  • 3.0.7
  • 3.0.6
  • 3.0.5
  • 3.0.4
  • 3.0.3
  • 3.0.2
  • 3.0.1
  • 3.0.0

1

Kumaran Baskaran, Jonathan R Wedell, Eldon L Ulrich, Jeffery C Hoch, and John L Markley. PyBMRB: Data visualization tool for BioMagResBank. In Meghann Agarwal, Chris Calloway, Dillon Niederhut, and David Shupe, editors, Proceedings of the 20th Python in Science Conference, 59–62. 2021. URL: http://conference.scipy.org/proceedings/scipy2021/pdfs/kumaran_baskaran.pdf.

2

Eldon L. Ulrich, Hideo Akutsu, Jurgen F. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F. Schulte, David E. Tolmie, R. Kent Wenger, Hongyang Yao, and John L. Markley. BioMagResBank. Nucleic Acids Research, 36(suppl_1):D402–D408, 11 2007. URL: https://doi.org/10.1093/nar/gkm957, arXiv:https://academic.oup.com/nar/article-pdf/36/suppl\_1/D402/7635401/gkm957.pdf, doi:10.1093/nar/gkm957.

3

Eldon L Ulrich, Kumaran Baskaran, Hesam Dashti, Yannis E Ioannidis, Miron Livny, Pedro R Romero, Dimitri Maziuk, Jonathan R Wedell, Hongyang Yao, Hamid R Eghbalnia, Jeffrey C Hoch, and John L Markley. NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments. Journal of Biomolecular NMR, 73(1):5–9, feb 2019. URL: https://doi.org/10.1007/s10858-018-0220-3, doi:10.1007/s10858-018-0220-3.