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rugnux: always write both MTZ and CIF; drop --scaling-output

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The merged reflections were written in one of mtz/cif/txt selected by
--scaling-output. Write both an MTZ and an mmCIF unconditionally instead - each
has its uses downstream (MTZ for the CCP4/phenix tools, mmCIF for deposition) -
and remove the format selector, the plain-text .hkl writer, and the now-unused
IntensityFormat enum / ScalingSettings::FileFormat plumbing.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-07-16 10:45:08 +02:00
co-authored by Claude Opus 4.8
parent ce12d69751
commit eae7ea90dc
7 changed files with 7 additions and 67 deletions
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docs/CHANGELOG.md
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@@ -21,6 +21,7 @@ This is an UNSTABLE release. It includes many experimental features, as well as
* Reader: Treat a negative `total_flux` in a stored dataset as unknown/absent rather than a real (invalid) flux.
* Packaging: Build the self-contained Linux viewer against a static libdbus with glib disabled, so the `.tgz` no longer drags a tail of system `.so` dependencies; add parallel image-build and in-container viewer-verification scripts.
* rugnux: Write anomalous data as a standard CCP4 anomalous MTZ - one row per reflection with `IMEAN`, `I(+)`/`I(-)` (and the matching `F`/`F(+)`/`F(-)` amplitudes) - instead of two `IMEAN` rows per Bijvoet pair, so `aimless`/`mtz2sca`/ANODE read it directly. The non-anomalous MTZ output is unchanged.
* rugnux: Always write the merged reflections as both `<prefix>.mtz` and `<prefix>.cif` (each has its uses downstream - MTZ for the CCP4/phenix tools, mmCIF for deposition). The `--scaling-output` format selector and the plain-text `.hkl` output are removed.
### 1.0.0-rc.159
This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.
docs/RUGNUX.md
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@@ -45,8 +45,8 @@ the first pass.
[HDF5 / NeXus data format](HDF5.md) for the layout. Written by default only when **not** merging
(i.e. under `--no-merge`); add `--write-process-h5` to also write it when merging.
- Merging is **on by default** (`--no-merge` disables it). The merged reflections are written as
`<prefix>.cif` (mmCIF — the default), or `<prefix>.mtz` / `<prefix>.hkl` depending on
`--scaling-output`. Both the mmCIF and the MTZ carry the **refined unit cell** (from rotation
**both** `<prefix>.mtz` and `<prefix>.cif` (mmCIF) — each has its uses downstream (MTZ for the
CCP4 / phenix tools, mmCIF for deposition). Both carry the **refined unit cell** (from rotation
indexing) and the **space group determined from systematic absences** (constrained to the indexed
lattice symmetry). No-reference scaling additionally emits per-iteration `<prefix>_iterN_scale.dat`.
@@ -212,7 +212,6 @@ Scaling and merging:
| `--min-image-cc <num>` | Per-image CC limit, percent (default: no limit) |
| `--mosaicity <num>` | Diagnostic: fix the scaling mosaicity (°) instead of using the per-image seed |
| `--scaling-iterations <num>` | Scaling iterations with no reference data (default: 3) |
| `--scaling-output <txt>` | Reflection output format: `cif` (mmCIF, default) \| `mtz` \| `txt` |
| `-z, --reference-mtz <file>` | Reference MTZ (enables reference-driven scaling) |
| `--reference-column <label>` | Reference MTZ column to use (default: auto — F-model, else IMEAN/I/…) |
| `--write-process-h5` | Also write the (large) `_process.h5` when merging (default: only `.mtz`/`.cif`) |