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Updated: Dec 31, 2025

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
Published on: September 17, 2017
PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins
Daniel K Weber1, Songlin Wang1, John L Markley2
1Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Motivation:
Two-dimensional [15N-1H] separated local field solid-state nuclear magnetic resonance (NMR) experiments of membrane proteins aligned in lipid bilayers provide tilt and rotation angles for α-helical segments using Polar Index Slant Angle (PISA)-wheel models. No integrated software has been made available for data analysis and visualization.
Results:
We have developed the PISA-SPARKY plugin to seamlessly integrate PISA-wheel modeling into the NMRFAM-SPARKY platform. The plugin performs basic simulations, exhaustive fitting against experimental spectra, error analysis and dipolar and chemical shift wave plotting. The plugin also supports PyMOL integration and handling of parameters that describe variable alignment and dynamic scaling encountered with magnetically aligned media, ensuring optimal fitting and generation of restraints for structure calculation.
Availability And Implementation:
PISA-SPARKY is freely available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers of the SBGrid (https://sbgrid.org). The pisa.py script is available and documented on GitHub (https://github.com/weberdak/pisa.py) along with a tutorial video and sample data.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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