From ee4c23b9a26052e13619e8f1b9062a56fedbb4dd Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Wed, 2 Sep 2026 09:06:21 +0200 Subject: [PATCH] docs: the phenix label override, for the mmCIF as well as the MTZ 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) Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N --- docs/RUGNUX_INTEGRATION.md | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/docs/RUGNUX_INTEGRATION.md b/docs/RUGNUX_INTEGRATION.md index a1dc7cc16..846c6fc2d 100644 --- a/docs/RUGNUX_INTEGRATION.md +++ b/docs/RUGNUX_INTEGRATION.md @@ -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