Troubleshooting iNMR: Common Errors and How to Fix Them

Troubleshooting iNMR: Common Errors and How to Fix ThemiNMR is a powerful macOS application for processing and analysing NMR data. Like any specialized software, it can present occasional errors or confusing behavior. This guide walks through the most common problems users encounter with iNMR, explains their likely causes, and provides clear, step-by-step fixes and preventive tips.

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1. Installation and Launch Problems

Symptoms

• iNMR won’t start or crashes at launch.
• macOS reports the app is from an unidentified developer.
• The app launches but immediately quits.

Likely Causes

• Incompatible macOS version.
• Gatekeeper blocking unsigned apps.
• Incomplete installation or corrupted app bundle.
• Conflicting third‑party software (security tools, older libraries).

Fixes

1. Check compatibility:
   • Ensure your macOS version is supported by the iNMR version you installed. Visit the iNMR website or release notes for minimum requirements.
2. Bypass Gatekeeper safely:
   • Right-click (or Control-click) the iNMR app and choose “Open.” Confirm the dialog to allow the app if you trust the source.
3. Re-download and reinstall:
   • Delete the app from Applications, download a fresh copy from the official source, and reinstall.
4. Review crash logs:
   • Open Console.app → User Reports to inspect iNMR crash logs; note recurring error messages to search further or report to support.
5. Test without third‑party interference:
   • Disable security utilities temporarily (or boot into Safe Mode) to see if iNMR runs. If it does, re-enable them and narrow down the conflicting tool.

Preventive tips

• Keep macOS and iNMR updated.
• Install iNMR only from the official site.
• Avoid running multiple older NMR tools that modify system libraries.

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2. File Import & Format Errors

Symptoms

• iNMR doesn’t recognize your dataset.
• Data import fails with “unsupported format” or shows garbled signals.
• Missing fid, odd axes, or unexpected dimensionality after import.

Likely Causes

• Using incompatible or vendor‑specific binary formats.
• Transferred or corrupted files (FTP/text mode transfer).
• Wrong import settings (e.g., interpreting 1D as 2D).
• Data stored in zipped/archived formats not automatically uncompressed.

Fixes

1. Confirm file integrity:
   • Re-transfer files in binary mode if using FTP/SCP. Re-download from instrument if possible.
2. Use the correct import pathway:
   • For Bruker, Varian/Agilent, JEOL or other vendors, use the matching import option in iNMR. Some vendors require the entire directory structure (acqus, fid, pdata).
3. Convert formats if needed:
   • Convert vendor files to a standard format (e.g., Bruker → JCAMP or Varian → DTA) using vendor utilities or scripts before loading.
4. Unzip/extract archives:
   • Ensure data folders are fully uncompressed. iNMR may not auto-decompress nested archives.
5. Inspect header/meta files:
   • For Bruker, check acqus and procs files for acquisition parameters. Corrupted or missing headers can mislead the importer.

Quick checks

• Open the raw fid with a plain-text or hex viewer to confirm it’s not truncated.
• Verify expected dimensionality and sample temperature values in header files.

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3. Incorrect Chemical Shifts or Peak Positions

Symptoms

• Peaks appear at wrong ppm values.
• Referencing to TMS or internal standard fails.
• Spectra show shifts compared to expected literature values.

Likely Causes

• Incorrect spectral reference (frequency used for calibration).
• Wrong nucleus or spectrometer frequency setting.
• Digital offset or incorrect spectral width/zero-order phase.

Fixes

1. Set the correct spectrometer frequency (MHz):
   • Verify the nucleus (1H, 13C, 31P, etc.) and enter the exact spectrometer frequency in iNMR’s dataset parameters.
2. Re‑reference the spectrum:
   • Use a known internal standard peak (TMS, DSS) or residual solvent signal. Place the cursor on the standard and use the “Set Reference” or ppm calibration command.
3. Check digital offset (reference point):
   • Ensure the reference frequency and the spectral width/offset values match those recorded by the instrument.
4. Reprocess with correct parameters:
   • Reload the fid and apply the proper spectral width, SW (Hz), and reference offset before Fourier transform.

Example

• If a 1H spectrum acquired at 400.13 MHz is entered as 400.00 MHz, ppm positions will shift slightly; correct the frequency to restore accurate chemical shifts.

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4. Poor Signal-to-Noise, Baseline or Lineshape Problems

Symptoms

• Noisy spectra, ragged or sloped baseline, distorted peak shapes.
• Broadened or asymmetric peaks.

Likely Causes

• Insufficient scans (low S/N).
• Incorrect apodization/window function or phase corrections.
• Truncation artifacts due to abrupt fid end or poor zero-filling.
• Poor shimming, sample issues, or probe tuning problems.

Fixes (software)

1. Apply appropriate apodization:
   • Use exponential multiplication (line broadening 0.3–1.0 Hz for 1H) or Gaussian functions to trade resolution for S/N.
2. Zero‑fill:
   • Zero-fill to at least twice the number of points (often 2–4×) before FT to smooth the digital baseline.
3. Baseline correction:
   • Use polynomial or spline baseline correction functions in iNMR to remove sloping/artifacts.
4. Phase correction:
   • Perform automatic phase correction, then fine‑tune manually (zero‑ and first‑order phases).
5. Deconvolution/lineshape fitting:
   • For overlapping or broadened peaks, use fitting tools to extract accurate peak parameters.

Fixes (hardware/sample)

1. Increase number of scans (NS) to boost S/N.
2. Improve shimming and probe tuning:
   • Re‑shim the sample and retune the probe; poor shims cause broadened, asymmetric peaks.
3. Check sample concentration and purity:
   • Very dilute samples yield low S/N; impurities can produce baseline distortions.
4. Verify temperature stability:
   • Fluctuating temperature can broaden lines, especially for exchange-prone systems.

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5. Phase Correction and Imaginary Component Issues

Symptoms

• Peaks with dispersive (negative/positive) tails or large imaginary residuals.
• Automatic phase fails or leaves complex lines.

Likely Causes

• Wrong FT parameters or phasing algorithm limits.
• Unapodized fid or incorrect zero-order/first-order phase starting values.
• Misapplied baseline corrections before phase.

Fixes

1. Perform FT with default or recommended settings (apodization + zero-fill), then auto‑phase.
2. Manually adjust zero‑order (PH0) and first‑order (PH1) phase:
   • Zero‑order corrects phase across entire spectrum; first‑order corrects frequency‑dependent tilt.
3. Use the imaginary/real display toggles to understand residual artifacts.
4. If automatic phasing repeatedly fails, try