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rugnux docs: add the four options the table never listed

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--overlap, --overlap-minpk, --prediction-mosaicity and --rotation-scale are all
accepted by the program and two of them change what is integrated by default,
but none appeared in the options table - so the only way to find them was to run
the program with no arguments. Descriptions cut down from the usage text.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y5XisyYxmF8mUEQjzpMRe2
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leonarski_f
2026-08-25 07:13:13 +02:00
co-authored by Claude Opus 5
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commit 9b2b79aa73
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@@ -537,6 +537,9 @@ Integration:
| `--integration-high-resolution <num>` | High-resolution limit for prediction and integration. Omitted (or 0) means integration extends as far as the detector reaches — which is what the predictor can place on the detector anyway, since it rejects reflections that miss it. Set a value to integrate less than the detector offers |
| `--max-hkl <n>` | Predict reflections with \|h\|,\|k\|,\|l\| ≤ `n` (max 511). By default this is derived per crystal from the refined cell as `ceil(max(a,b,c)/d_min) + 1`, which is the exact bound: the predictor keeps only \|q\| ≤ 1/d_min and `h = a·q`, so no reflection can lie outside it and no candidate inside it is wasted on a shorter axis. Set it only to override that |
| `--bandwidth <num>` | Relative X-ray bandwidth FWHM (e.g. `0.01` for a 1% DMM); default from file or 0 (monochromatic) |
| `--overlap <txt>` | What to do where two predicted reflections share signal pixels: `off` \| `reject` \| `exclude` (default `exclude`). A shared pixel belongs to the nearer centre; without this a crowded reflection reads high on a dense pattern. `exclude` drops the shared pixels from the profile fit, which renormalises itself, and keeps the reflection; `reject` instead drops the whole reflection when too little of its profile is cleanly its own. `--integrator boxsum` has no profile to renormalise, so only `reject` acts there |
| `--overlap-minpk <f>` | Least fraction of a reflection's expected profile that must be usable for it to be kept (default 0.75, XDS `MINPK`). Governs both the fraction that must be **readable** — not masked, untrusted, in a gap or overloaded — in every profile mode, and, under `--overlap reject`, the fraction that must be cleanly its own. Under `--integrator boxsum` any unreadable pixel discards the disk outright and the reject fraction goes by disk *area*, which cuts harder |
| `--prediction-mosaicity <num>` | Diagnostic: fix the rocking width (deg) the **prediction** window opens to, leaving partiality on the per-image σ_M. The two are one number by default, so a σ_M that moves takes the integrated reflection population with it |
Geometry overrides (defaults are taken from the input file; override them to reprocess with a corrected geometry):
@@ -549,3 +552,4 @@ Geometry overrides (defaults are taken from the input file; override them to rep
| `--rot1 <num>` | PONI detector rotation 1 (rad) |
| `--rot2 <num>` | PONI detector rotation 2 (rad) |
| `--polarization <num>` | Polarization factor |
| `--rotation-scale <k>` | Goniometer rotation scale: the stage turned `k` times the angle stored in the file (the commanded one). Applied to both passes, and overrides the scale rugnux fits for itself |