2D Experiment Analysis
NMRAnalysis.jl provides interactive GUIs for analysing 2D NMR experiments, including relaxation, exchange, and NOE measurements. All functions follow the same pattern: they load one or more processed 2D spectra, open an interactive window for peak picking and fitting, and export results to a folder of your choice.
The experiment-specific pages describe the available functions and the theory behind each analysis. This page covers the shared GUI features common to all of them.
Adding and Managing Peaks
Peaks are picked interactively using the mouse and keyboard. Move the cursor over a peak in the contour plot to work with it.
| Action | Key / Button |
|---|---|
| Add peak at cursor position | A |
| Track peak from cursor position | T |
| Delete the selected peak | D or Delete peak button |
| Rename the selected peak | R or Rename peak button |
| Navigate to previous spectrum slice | ← or ← button |
| Navigate to next spectrum slice | → or → button |
| Raise contour base level | ↑ or contour ↑ button |
| Lower contour base level | ↓ or contour ↓ button |
| Reset axis zoom | reset zoom button |
| Show or hide the fitted lineshape overlay | Fitting toggle |
| Open a summary plot of the current results | Summary plot button (enabled once peaks are present) |
| Load a previously saved peak list | Load peak list button |
| Save all results to a folder | Save to folder button |
| Close the GUI window | Quit button |
Peak lineshapes are fitted in real time as you add or move peaks. The right panel shows cross-sections (or a model fit plot, for relaxation-type experiments) for the currently selected peak.
Visual Feedback
The window background changes colour to indicate the current interaction mode:
| Background | Mode |
|---|---|
| White | Normal |
| Salmon / orange | Fitting in progress (save operation) |
| Light blue | Renaming a peak |
| Pale green | Moving a peak |
Peak markers are colour-coded:
| Colour | Meaning |
|---|---|
| Blue | Unmodified peak |
| Red | Manually moved or adjusted peak |
| Green | Currently selected peak |
Recommended Workflow
- Launch the appropriate analysis function with your input files.
- Navigate to a representative spectrum using
←/→or the slice slider. - Adjust contour levels with
↑/↓until peaks are clearly visible. - Add peaks with
Aat each resonance you want to track. - Optionally rename peaks with
Rto match residue assignments. - Navigate through all slices to verify fit quality across the series.
- Click Save to folder to write all output files to a chosen directory.
For large datasets, it is efficient to pick peaks on one representative slice first, then step through remaining slices to check that the fits are good.
Output Files
Clicking Save to folder writes the following files:
| File | Contents |
|---|---|
results.csv | One row per peak: positions (δ₁, δ₂), linewidths (R2x, R2y), per-plane amplitudes, and any derived experiment parameters (relaxation rates, NOE values, …), each with uncertainties |
summary.pdf | Summary plot of the primary fitted parameter against residue number (or atom for methyl/non-backbone experiments) |
peak_LABEL.pdf | Per-peak publication-quality fit plot for each labelled peak |
cluster_LABEL.pdf | Zoomed 2D contour plot (first plane) with fitted lineshapes for each group of overlapping peaks |
results.csv has experiment metadata in #-comment lines above an ordinary header row, so it opens directly in spreadsheets and pandas. Existing files are backed up with an .old extension before being overwritten. See Peak Lists and Output Files for the full column description.
Loading and Resuming Analysis
The Load peak list button restores peak positions and labels from a saved results.csv (or a simple label x y text file), so you can resume work later or seed a new analysis from existing positions. Only the label, x and y columns are read — see Peak Lists and Output Files.
Summary plots
summaryplot plots a fitted parameter against residue number, from a live experiment or one or more saved results.csv files. See the Summary Plots page for full details and examples.
Adjusting the Fitting Region
The X and Y radius sliders in the peak info panel control the size of the region around each peak used for lineshape fitting. Smaller radii are appropriate for crowded spectra; larger radii improve the fit for broad peaks.