Welcome to the pyDIFRATE tutorial

pyDIFRATE is software originally developed for analyzing NMR relaxation rate constants with minimal assumptions about the form of the correlation function. It uses the “Detectors” approach, to return amplitudes of motion for timescale-specific windows. It has been broadly expanded to also analyze MD simulations. These analyses include direct comparison with NMR results, timescale-specific cross-correlation of motion, and separation of motion via frames (ROMANCE analysis). A principal component analysis module is also underway.

These features are coupled with powerful visualization methods, including 3D visualization on the structure with ChimeraX, and with a file management system to keep track of data processing steps and help with data sorting and comparison.

The tutorial here provides explanation of the detectors motivation, and some basic explanation of the theory, as well as example analyses. A series of templates are also provided into which one may insert ones own data, and can either be downloaded or run on Google Colab. Running on Colab means you do not need to provide your data to our servers, nor is it stored by Google beyond the lifetime of the session.

• Getting Started
• Background
• References

Tutorial

• Chapter 1: A brief introduction to detectors
• Chapter 2: Detector Optimization
• Chapter 3: A Basic NMR Analysis
• Chapter 4: Comparison of Model-Free, SDM, LeMaster’s Approach, and Detectors
• Chapter 5: Comparing MD and NMR Results
• Chapter 6: Anatomy of pyDIFRATE
• Chapter 7: Cross-Correlated Dynamics via iRED
• Chapter 8: ROMANCE Analysis of Backbone Motion

Templates

• Template: pyDR Setup
• Template: Basic NMR
• Template: Solution-State NMR
• Template: Cross-Correlated Dynamics via iRED

HET-s(218-289) Dynamics NMR data analyzed via detector analysis and plotted with NGLview (built into pyDR). The detector near 6 ns is shown