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docs: the phenix label override, for the mmCIF as well as the MTZ

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Both merged formats hit the same refusal - the file carries the mean and the
Bijvoet pairs - but the label vocabularies differ per format and the MTZ
incantation fails on the mmCIF with a fresh error. Give both measured
commands, and say it is one behaviour in two formats, not a difference
between our files.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
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leonarski_f
2026-09-02 09:19:16 +02:00
co-authored by Claude Opus 5
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docs/RUGNUX_INTEGRATION.md
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@@ -120,16 +120,21 @@ independently determined orientation matrix agrees with rugnux's to well under a
The reflection files are inputs to other suites, and the handover has a few conventions worth one
line each. These are the minimum commands that get each program running on rugnux output.
**phenix.** The merged MTZ carries both `IMEAN` and `I(+)`/`I(-)`, and phenix refuses to choose
between two equally usable intensity arrays (`Multiple equally suitable arrays of observed xray
data found`) — name the array, noting that the two programs take different parameter names for the
same choice:
**phenix.** The merged files carry both the mean intensity and the Bijvoet pairs, and phenix
refuses to choose between two equally usable intensity arrays — `Sorry: Multiple equally suitable
arrays of observed xray data found.` (from the mmCIF the message at least lists the choices; from
the MTZ it names none, which is where a user is genuinely stuck). It is one behaviour surfacing in
both formats; only the label vocabulary differs, following each format's own column names — the
MTZ label fails on the mmCIF with `Sorry: No matching array`:
```
phenix.xtriage myrun.mtz xray_data.obs_labels=IMEAN,SIGIMEAN
phenix.xtriage myrun.cif xray_data.obs_labels=intensity_meas
phenix.refine model.pdb myrun.mtz miller_array.labels.name=IMEAN
```
(phenix.refine takes a different parameter name for the same choice.)
**The R-free convention.** `FreeR_flag` is **0 = work, 1 = free** (the phenix/CNS convention;
5 % free by default). phenix.refine detects that on its own. **REFMAC5 does not**: its default
takes flag 0 as the free set and stops with `Error ==> Cannot switch free R flag` — give it the