Software & methods

Made for discovery.

Practical tools for molecular questions.
Explore structures. Analyze interactions. Design experiments.

Molecular visualization

MolApp.

A closer look.
Wherever you are.

Explore protein and molecular structures in 3D. Open PDB and mmCIF files, choose representations, and measure molecular geometry with a Mol*-powered viewer.

Available as MolApp on Google Play and MolViewApp on the App Store. Scan a QR code, or select a store below.

TROSY for rotational correlation times

TRACT.

A quick look at protein tumbling.
Estimate effective rotational correlation times from ¹⁵N–¹H relaxation interference.

Download the toolkit
TRACT¹⁵N–¹H relaxation
1.00.500Relaxation delayNormalized intensity
α spin stateβ spin state

Schematic illustration · not experimental data

Three files. One workflow.

Original pulse program, analysis worksheet, and data-splitting script.

Read the guide

Bruker pulse program

¹⁵N–¹H TRACT sequence, with water-flipback and WATERGATE settings.

tract.dl · 3.0 KB
Download pulse program

Correlation-time worksheet

Original Excel worksheet relating spin-state relaxation rates to τc.

tract.xls · 39.5 KB
Download worksheet

Interleaved data splitter

Perl utility for separating an interleaved Bruker ser file.

split_all_int.pl · 723 bytes
Download script

From experiment to insight.

01   Set up the experiment

Use tract.dl as the original sequence reference. Calibrate the pulses, gradients, carrier, and water suppression for your instrument and sample. The file documents p1, p5, p11, sp1, sp2, and the relaxation-delay increment. Compatibility with a particular TopSpin release must be checked on the instrument.

02   Separate and process the data

The legacy split_all_int.pl script reads ./ser and writes ./ser1 and ./ser2 with its supplied settings. It assumes 4-byte data points, 1,024 direct-dimension points, and 20 delay points. Edit initnr, endnr, tdpoints, and directtdpoints to match the acquisition. Run it only on a working copy in a folder without existing output files; it overwrites files with those names.

Process the separated decay series and determine the α- and β-spin-state relaxation rates. The splitter itself does not fit relaxation data.

03   Estimate the correlation time

Open tract.xls in a compatible spreadsheet application. Review the field and physical constants, and replace the example relaxation rates with measured values. The supplied sheet contains a 750 MHz example, Rβ = 64 s⁻¹ and Rα = 13 s⁻¹.

The worksheet presents a cubic equation in τc; select the physically meaningful positive root and check units. Its stored result is an example, not an automatic browser calculation or a result for your sample.

What does TRACT measure?

TRACT uses the difference between spin-state relaxation rates to estimate an effective rotational correlation time. It is useful for assessing sample behavior and planning NMR experiments. Internal motion, anisotropic tumbling, and experimental conditions affect interpretation; τc should not be treated as a direct molecular-weight measurement.

Please cite the original method.D. Lee, C. Hilty, G. Wider, and K. Wüthrich. “Effective rotational correlation times of proteins from NMR relaxation interference.” Journal of Magnetic Resonance 178 (1), 72–76 (2006).
doi:10.1016/j.jmr.2005.08.014 ↗

The three original files are distributed unchanged. File checksums are included for verification. This is a legacy research toolkit; instrument operation and numerical validation remain the user’s responsibility.

Protein excited states

ONEST.

A web-based platform for rapid, robust analysis of protein excited states through chemical exchange saturation transfer (CEST) spectroscopy.

Web application · CEST

Relaxation dispersion

ShereKhan.

Analyze NMR CPMG relaxation-dispersion curves with two-state chemical-exchange fitting, including exact matrix, slow-exchange, and fast-exchange models.

Explore on GitHub
Python · Open source

Pulse program selection

pp_selector.

Type pp_selector on the TopSpin command line, answer a few questions about your sample and the information you need, and receive a recommended Bruker standard pulse program with its parameter set. It only displays the recommendation and never changes the current dataset.

Explore on GitHub
TopSpin 3.x–5.x · Jython · Open source

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