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Monodisperse analysis

Open this window from the right-column monodisperse icon. While it stays open, new samples that reach a calibrated (and optionally subtracted) 1D profile run Guinier → P(r) / GNOM automatically. Closing the window disarms that chain.

Each pane shows a plot (or plots), a Passport table of quality metrics, and an Adjust button. Parameter controls live in dedicated adjust wizards — not on the main pane. Optional shape modeling (BODIES / DAMMIF / DENSS) is launched with Start modeling into a separate Shape Modeling app — press Confirm there to run.

Opening an Adjust wizard and changing controls (or confirming) pauses auto-processing until you Resume auto-processing (Ctrl+P; Ctrl+X stops auto). Guinier artifacts for this window live under guinier_mono/ (separate from polydisperse).

Monodisperse analysis window

Layout

Guinier — Guinier plot; Passport (fit quality, low-q classification, Rg, q-range, …); Adjust opens the Guinier adjust wizard (first/last live there).
P(r) — embedded I(q) and P(r) plots; Passport (status, Total est., χ², Rg, D_max, …); Adjust opens the P(r) / GNOM wizard (or click either plot).
Shape — None / BODIES / DAMMIF / DENSS; Start modeling opens the Shape Modeling app; I(q) fit and 3D preview; Open model folder… when artifacts exist; mode-specific knobs (e.g. DAMMIF n_runs, DENSS protocol) apply on the next modeling run.
Global — Stop auto-processing / Resume auto-processing (Ctrl+X / Ctrl+P).

Recipes

To arm monodisperse analysis

Main window right → monodisperse icon → window opens (armed while open).

Main window with analysis icons

To adjust Guinier limits

Click Adjust under the Guinier passport (or the Guinier plot) → edit first / last in the wizard → plots and passport update live → Confirm to write parameters and re-run Guinier (then GNOM for the current profile). Restore auto returns to the auto-chosen interval. Click a wizard plot to open an enlarged viewer (matplotlib toolbar + title-bar maximize).

Guinier adjust wizard

To adjust P(r) / GNOM

Click Adjust under the P(r) passport (or either embedded P(r) / I(q) plot) → dedicated wizard with P(r), I(q) fit, residuals, q_min/q_max, D_max, alpha, boundary checkboxes, and passport. Plots and passport update live as you edit; press Confirm to write parameters and re-run fit_distances. Use Restore auto for the auto-fit Dmax/alpha snapshot. Click a wizard plot for an enlarged viewer (title-bar maximize). Resume auto-processing when ready; re-run shape modeling if needed.

P(r) / GNOM adjust wizard

To enable shape modeling

Under Shape, choose BODIES, DAMMIF, or DENSS (and options as needed) → Start modeling → Shape Modeling app opens → set run knobs → Confirm there. When the Shape Modeling app is open and auto is on, new profiles that finish GNOM can prompt Confirm on that app. Use Open model folder… for on-disk 3D outputs. Click the 3D preview for an interactive viewer when a model exists.

To pause or resume the auto chain

Stop auto-processing (Ctrl+X) → new files skip analysis until Resume auto-processing (Ctrl+P). Editing/confirming an Adjust wizard also moves you into Manual until you resume.

Outputs (per sample)

guinier_mono/<stem>/ — Guinier region / quality
fit_distances/<stem>/ — GNOM .out, p(r) / fit plots, quality YAML
model_bodies/, dammif/, or denss/ under the stem when shape modeling has run

Polydisperse → · Algorithms: Guinier · p(r)