HELP / PRIME 0.10.1
From your first spectrum to the report.
Instructions, screenshots and review criteria for Prime. Find a task, follow the application controls and preserve result provenance.
24 chapters · search · print · expandable screenshots
Spanish interface, Spanish and English help. Screenshots use a real experimental ramp; the PS conversion is exploratory and settings windows are not new measurements.
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01 · Choose a product and start
Prime is the general-purpose diffusion workspace. ResinAtOnce retains the resin-specific workflow.
- Open your existing Windows Prime package; check the executable version. This website does not enable a new public download.
- Open Bruker data or a .prime.json project. Use Synthetic demo only to learn the interface.
- Follow acquisition → preparation → calculation → review → save → report.
23 experimental TP194 spectra in CDCl₃; ramp 10–32. Saved TRAIn map, TTMS standard and active projection. Residual and status describe this calculation, not universal validation.
A general-purpose interface does not make molecular calibrations universal. Review each model’s medium and domain.
02 · Import a Bruker ramp
The supported import route reads processed 1r spectra, retaining amplitudes and metadata.
- Select Open Bruker and the acquisition with numbered experiment folders. Set ramp, pdata number and points per bin.
- Review title, nucleus, solvent, sequence, TE, RG, NS, probe and gradients. Do not combine incompatible acquisitions.
- Use binning 1 to retain full resolution; binning speeds up calculations but changes the averaged region.
Measured spectra and local region. Common scaling and signal sign are retained; experiments are not individually normalised to match.
This is not a universal FID/ser processor: do not assume automatic FT/phase or SPEN reconstruction. Originals are unchanged.
03 · Navigate, zoom and change theme
Spectrum, map and projection share context; the side panel holds the controls.
- Use Theme ◐ for light/dark and Focus F11 to give the map more space. Effects can be disabled.
- Fit signals frames visible bands; Full range restores the entire axis. Use the wheel to zoom.
- The visual threshold is at the upper right. Change Original/Model through representation settings.
Changing theme does not change intensities, calibration, representation or results.
Zoom, theme and threshold are display controls: they must not change the data, selected representation or quantitative moments.
04 · Probe and b encoding
Probe detection and gradient calibration are separate decisions.
- Open Probe / calibration. Automatic reads PROBHD; a documented manual label is also available.
- Retain reviewed b or import a b manifest in s/m². You may also review Gmax or calibrate with a known solute in the same medium and temperature.
- Preview factors and b by experiment, document the source and apply to a derived copy. Recalculate afterwards.
Calibration window for the real case; no changes applied. A probe label does not determine Gmax.
The rectangular PGSE formula is not valid for every sequence. The shared experimental TBO calibration is protected; a detected probe does not authorise nominal Gmax.
05 · Solvent, temperature and viscosity
Open Prepare DOSY / MwOSY → Medium / temperature.
- Check detected SOLVENT and TE. Select an available correlation or enter manual viscosity with source and Pa·s units.
- Use fixed η at a reference temperature (293 K proposed) or temperature-dependent η. Confirm applicability to your composition.
- Thermal normalisation of D is a separate option: choose output temperature and law. Check factors before applying.
Settings for the real acquisition. Pure-solvent viscosity is a reviewable approximation, not a measurement of the mixture.
The ten solvent curves come from the documented package sources. A pure/non-deuterated analogue does not measure the viscosity of a concentrated mixture. Rh requires reviewed η.
06 · TTMS and multiple internal standards
Detecting a signal does not mean approving a standard.
- Open Internal standards and select Detect / recheck. Review position, attenuation, local D and documented Rh.
- Confirm which substance you added and its region. The laboratory TTMS protocol uses Rh = 3.65 Å, conditional on identity and medium.
- If expected D is missing, review η(Tref) beside the standard. For multiple standards, use Manage multiple and check compatibility before enabling them.
Detection on the real ramp and saved settings. A ppm candidate does not confirm which substance was added.
Compatible factors are combined; overlapping or discordant standards require review. Do not force each standard to its expected value using individual factors.
07 · Calculate without an internal standard
An internal standard is optional, not a prerequisite for D.
- Disable Apply confirmed standards or choose the no-internal-standard mode.
- Review b, temperature and remaining assumptions; recalculate.
- Check WITHOUT INTERNAL STANDARD in the result and report. Standard definitions can remain saved.
Unchecking a box does not retroactively remove calibration from a saved result. New settings take effect when recalculating.
08 · Apply corrections without duplication
Prime retains measured D, fReference, fTemperature and their product.
- Use Check factors to preview. Save parameters does not replace the previous result.
- Apply and recalculate archives the previous state and recalculates maps and regions with the same settings.
- Review final D = measured D × fReference × fTemperature and the associated conditions.
A temperature correction is not a convection correction. Do not use the same solute to calibrate b and correct D again without checking double counting.
09 · Calculate DOSY and select a method
Calculate map uses edited method and conditions; the previous map retains its own.
- Choose coherent TRAIn, MF-NNLS256, TRAIn-MF, RAI-S, DOME-S, SILT or the local Diffusion-Inversion route for your problem.
- Review ppm interval, D range, bins, iterations and regularisation. TRAIn uses termFac; it is not the same parameter as λ.
- Calculate and inspect convergence, residual and attenuations. Use Cancel to interrupt; the last complete result is retained.
23 experimental TP194 spectra in CDCl₃; ramp 10–32. Saved TRAIn map, TTMS standard and active projection. Residual and status describe this calculation, not universal validation.
Different methods optimise different objectives and may disagree. Do not change parameters just to get a convergence flag or force equal bands.
10 · Omitted or rejected attenuations
The detector evaluates noise, useful signal and attenuation coverage.
- Open Attenuations. Check whether a column is continuous, discrete, a standard, excluded or omitted, and read its reason.
- If no attenuations are accepted, select a diagnostic row to inspect its exact points and noise estimate.
- Review phase, baseline, region and b; save the diagnostic. Adjust policy only with experimental justification.
An empty map is not saved as a result. Attenuation that disappears too early does not thereby contain enough distribution information.
11 · Double-click: calculate a specific peak
The marker identifies the local maximum in the lowest-b spectrum; extraction stays fixed throughout the ramp.
- Zoom into the region and double-click the peak. Check the marker and extraction half-width.
- Calculate D / Mw and distribution runs inversion. D only gives a monoexponential fit, not a distribution.
- Review the values and use Add to results; then save the project.
Experimental region centred at 4.4182 ± 0.04 ppm. TRAIn is calculated on original signed data; standards are markers with no area.
A different maximum is not followed in each experiment. A monoexponential D marker is not turned into an invented distribution curve.
12 · ln(I/I₀) and linear regression
The linear tab is available before inversion.
- Open ln(I/I₀) · linear fit and points. Read slope, intercept, R², measured/final D and OLS error.
- Review I₀ and b₀: they come from the positive point at the lowest available b. The horizontal axis is (b−b₀)/10⁹ and the intercept is free.
- NaN/Inf, invalid b or I≤0 are excluded only from the logarithm, with a reason in the table.
OLS fit to every valid point in the experimental region. I₀ is the positive intensity at the lowest available b.
Log-space OLS and intensity fitting minimise different errors. OLS error excludes calibration, selection and convection uncertainty.
13 · Automatic and manual point selection
Review compares all valid points with the selected subset and keeps exclusions visible.
- Automatic · improve R² searches within limits: by default ≥6 points, ≥80% b coverage and ≤20% valid-point exclusions.
- For manual decisions, select rows and press Apply manual selection. All valid restores the baseline fit.
- Save the linear fit to include it in the project and report, with mask, reasons and comparison.
Exploratory R²-based selection. Excluded points remain visible; the mask does not affect inversion or the map. Higher R² does not prove a more accurate D.
Improving R² may bias D. Selection is exploratory, not proof of absent convection or an automatic mask for TRAIn, Tikhonov or MaxEnt.
14 · Distributions, regularisation and components
A 1D distribution describes a specific region; it is not the projection of the entire map.
- Select local method, grid and parameters. Reset parameters proposes values; it does not validate their optimality for your sample.
- Compare signal/prediction, residuals, boundaries and sensitivity to λ or termFac. A non-converged iterate is diagnostic.
- In Separate components, review valleys, descriptive Gaussians, residual and component moments. Original bins are retained.
Descriptive separation of the calculated distribution. Moments use assigned bins, not Gaussian tails or identified chemical species.
The number of modes depends on resolution and regularisation. It is not the number of compounds or their concentrations.
15 · Compare local TRAIn and DOSY
Use Local signal · TRAIn / compare to inspect the original bin and its settings.
- Select the same interval, ppm binning, acquisitions, b, method, grid and parameters.
- First compare measured D and original distribution; then fReference and fTemperature.
- Distinguish local components, MF rank and global-projection bands. They are different objects.
A difference between a global band and a local region is not itself an error. Numerical agreement requires identical inputs and objectives.
16 · MwOSY: choose the molecular calibration
Changing the axis does not turn apparent mass into validated absolute mass.
- In Prepare DOSY / MwOSY → 3 choose D, high-dilution PS, high-dilution PPG, shared concentration or a custom curve.
- PS and PPG are two high-dilution curves. There is one concentration model, developed with PS; it does not depend on choosing PS/PPG.
- Review viscosity, temperature, conditions and domain. The shared implementation requires ¹H/CDCl₃ and output near 293 K; other media require a custom calibration.
MwOSY view derived from the experimental map with the high-dilution PS curve. An apparent-mass conversion example: it does not identify TP194 as PS or validate its absolute mass. No weighing data were invented.
A small standard calibrates D, not the D–M relation of every polymer, star or brush. The PS screenshot is an exploratory conversion, not the sample’s identity.
17 · Weighings and concentration
Only the concentration model needs C = solute mass / solvent mass, in mg/mg.
- Prime looks for masses with units in the title of the first experiment in the ramp. They may occur anywhere in the text.
- The first is solute; the second is solute + solvent. Subtract them to obtain solvent. mg/g and decimal comma/point are supported.
- If information is missing or ambiguous, fields remain empty. Enter both weighings or explicitly review a historical C; zero is not invented.
Arithmetic example, not screenshot data: 7.52 mg and 827.09 mg → 819.57 mg solvent → C ≈ 0.00917554 mg/mg. This is neither percent nor mg/mL.
18 · Gaussian field and active projection
Modelling is descriptive and retains positive unfitted signal.
- Gaussian modelling + retained signal is enabled by default. Change it in advanced settings.
- The projection is recalculated from the active representation. Review error, visually added area and model residual.
- Select a projection band or map cross-peak. Inspect peak, mean and Rh or mass moments for the complete band.
Gaussians and bands do not prove chemical species. Visual threshold and band selection must not erase original signals or change saved results.
19 · Review and apply alignment
Beatrix flags possible shifts; the application never aligns without review.
- Open Review / align and compare intervals, experiments, shifts and before/after attenuation.
- Adjust anchor and limits if needed. Unresolved means the method lacks sufficient evidence to shift that case.
- Confirm your reason and create an aligned copy. The previous state is archived; review standards and recalculate results.
iCOshift-Prime review of the experimental spectra; no alignment applied. Unresolved cases do not mean there is no drift.
iCOshift-Prime is a modified in-house C# version, not official iCOshift 3.0. Alignment neither corrects convection nor validates overlapping-component areas.
20 · Convection diagnosis and review
Diagnosis distinguishes detected, not detectable and inconclusive.
- Select the signal and open R&D → Analyse ramps from this preparation. Compatible ramps and known calibration are required.
- Read Guide and final correction: noise, sequence moments, stability and sensitivity must meet the requirements.
- Where eligible, calculate physical inversion or document another control acquisition. Explicitly activate the final revision for that signal.
The entire map is not automatically rescaled. The report distinguishes physical correction, another control measurement and no correction. High R² does not rule out convection.
21 · Beatrix and assignment suggestions
Cards start from the same peak, band and result you are viewing.
- Hover over a signal to see hypotheses. Click to pin context and open cards and sources.
- Review nucleus, solvent, accompanying windows, multiplicity and other band cross-peaks. Open the source before assigning.
- History is labelled historical. Pause prompts or configure local AI/API providers; keys are not part of the project.
Experimental aromatic region. Documentary suggestions, such as a phthalic fragment, require checking other signals; they are not automatic identifications.
The catalogue contains polymer/resin fragments and impurities, not all chemistry. A match is neither identification nor probability. GPU/API connectivity depends on the provider; no newly validated fine-tuning is claimed.
22 · Local library, HTTP and external algorithms
Local Diffusion-Inversion and an HTTP connection are different routes.
- The local selector runs the bundled C# library without an HTTP server or MATLAB. Review parameters for each method.
- For HTTP, configure the endpoint and JSON/SI contract. Review data leaving the computer and authorise the request.
- An external executable requires path, arguments, hash and timeout. Inspect the response before using it.
Not every endpoint or executable is compatible. External results are not automatically applied to the map or considered validated because they came from an API.
23 · SPEN, ultrafast and published examples
These modalities have a research area, not a promise of universal reconstruction.
- Open Examples and references to inspect SPEN-DOSY and UF-DEXSY with DOI, licence and SHA-256.
- Consult original sources for sequences, echo order, kernel, spatial reconstruction and units.
- The user’s new ultrafast DOSY sequence is untested. Use its reviewed experimental contract, never conventional b as a silent substitute.
Actual application library: published SPEN-DOSY and UF-DEXSY packages with DOI, licence and hashes. This screen is not a reconstruction of those experiments.
UF-DEXSY studies diffusion/exchange, not a ppm–D map. Inspecting a published package does not mean Prime has reconstructed or validated those data.
24 · Batches, projects and reports
The saved result, not a pending edit, is the basis of traceability.
- In Ramps / batch choose ramps and review each set of conditions. Errors and cancellations are recorded.
- Save the .prime.json project. Reusable settings retain algorithm parameters, not sample identity or transferable calibration.
- Export report creates a new revision with editable DOCX, HTML, CSV and JSON; PNG from the view, a manifest and completion marker.
If editing and result differ, recover map parameters or recalculate. Do not mix another ramp’s result with the current selection. Review the report before sharing it.
Before communicating a result
- Correct sample, ramp, region and method.
- Measured D and factors separated; standard use or absence visible.
- Mass model, viscosity and concentration documented.
- Convergence, residuals and convection reviewed; hypotheses not presented as identities.
- Project saved and DOCX/HTML checked.
DIFFATONCE / MOLECULAR DIFFUSION