Peak Lists and Output File Formats
All 2D analyses read a peak list as input and write their results to a single file. This page describes both, and the recommended (but not enforced) way to label peaks.
Recommended labelling
Any labelling convention is accepted — the parser never rejects a label. However, the following conventions let the software extract residue numbers and atom types for sorting and summary plots:
| Group | Pattern | Examples |
|---|---|---|
| Backbone amides | one-letter code + residue number | G10, S11, I13 |
| Methyls / sidechains | … + atom name | I13CD1, L26CD1, L26CD2, V70CG1, M98CE |
| Nucleic-acid atoms | … + atom name | A12C8, G5C1' |
Peaks whose label does not begin with a standard residue code — including the default X1, X2, … given to newly picked, unassigned peaks — are assigned a negative residue number and are omitted from residue-number summary plots by default.
Input: peak lists
A peak list tells the software where the peaks are. The only information the reader needs is, for each peak, a label and its two chemical shifts (x = direct/F1, y = indirect/F2, in ppm). Everything else is derived from the label or measured by fitting.
The simplest input is a plain three-column text file, one peak per line:
G10 8.40 121.0
S11 9.02 115.7
I13 7.65 119.3Fields may be separated by spaces, tabs, or commas. Lines beginning with # are ignored. No header is required.
You can also load a previously saved results.csv (see below) to resume work or to seed a new analysis from existing positions — the reader takes the label, x and y columns and ignores the rest.
When a file is loaded, only the label and the two chemical shifts are used. Residue number, residue type, atom name, linewidths, amplitudes and derived parameters are all ignored on input (the residue number and atom are re-derived from the label). You never have to reproduce those columns to re-use a file as input.
Output: results.csv
Clicking Save to folder writes a single file, results.csv, with one row per peak. Experiment metadata is written as #-comment lines, followed by an ordinary header row and the data:
# Analysis type: Heteronuclear NOE
# Filename: /path/to/data
# Number of peaks: 3
label,resnum,resname,atom,x,x_err,y,y_err,R2x,R2x_err,R2y,R2y_err,amp[1],amp[1]_err,amp[2],amp[2]_err,hetnoe,hetnoe_err
G10,10,G,,8.40,0.01,121.0,0.05,30.1,1.2,15.2,0.8,4.5e5,2e3,3.6e5,2e3,0.78,0.04Because the header is a real (uncommented) row, the file opens directly in a spreadsheet and is read by, e.g., pandas.read_csv("results.csv", comment="#").
The columns are:
| Column | Meaning |
|---|---|
label | Peak label (editable in the GUI) |
resnum | Residue number derived from the label (negative for unassigned peaks) |
resname | One-letter residue code derived from the label |
atom | Atom name derived from the label (blank for backbone amides) |
x, y | Fitted chemical shifts (ppm), each with an _err uncertainty |
R2x, R2y | Fitted linewidths in the direct/indirect dimensions (s⁻¹) |
amp[i] | Fitted amplitude in spectrum/plane i |
| derived | Experiment-specific results (e.g. hetnoe, R20, PRE, eta, R) |
Per-plane quantities are indexed in square brackets (amp[1], amp[2], …). A single-spectrum analysis has just amp[1]. The same name[i] convention would extend to positions (x[i]) if a future analysis allowed peak positions to vary between planes.
Each value column is immediately followed by its uncertainty (value, value_err). The derived experiment parameters appear last, with the primary result first. Existing files are backed up with an .old extension before being overwritten.
results.csv is both the results table (for plotting and downstream analysis, e.g. with summaryplot) and a valid input file (for reloading peak positions).
Plotting summaries
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.