From 63a2f6744a23ffe88f54339a545d97a88a01a659 Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Wed, 2 Sep 2026 14:49:10 +0200 Subject: [PATCH] docs: say what the MTZ base-dataset fix actually changed, and what it did not The page said the fix makes mtzinfo and mtzdmp report the collection wavelength, which implies mtzdmp was wrong before. It was not. Verified across 226 files from two battery arms, one built before the fix and one after: every pre-fix merged MTZ reports 1.54187 under mtzinfo and the true wavelength under mtzdmp, truncate, ctruncate, gemmi, iotbx and phenix.xtriage. No program was found whose output or behaviour differs between the two files - cad silently repairs the layout on the way through. So the fix buys a conformant file and a correct mtzinfo line, not a rescued phasing run, and the f'/f'' consequence is the risk it removes rather than a measured effect. Also records that _unmerged.mtz still reads 1.54187 under mtzinfo and is not a regression: its columns sit on HKL_base deliberately, which is what POINTLESS expects, and the per-batch wavelength AIMLESS and POINTLESS actually read is correct. Co-Authored-By: Claude Opus 5 (1M context) --- docs/RUGNUX_INTEGRATION.md | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/docs/RUGNUX_INTEGRATION.md b/docs/RUGNUX_INTEGRATION.md index 0bcf2b6c6..5ecc41909 100644 --- a/docs/RUGNUX_INTEGRATION.md +++ b/docs/RUGNUX_INTEGRATION.md @@ -58,9 +58,14 @@ H H H J Q K M K M F Q G L G L ``` `F` is the French–Wilson amplitude. The header carries the determined space group, the refined cell -and the wavelength, on a dataset of its own behind the reserved `HKL_base` — so `mtzinfo` and -`mtzdmp` report the wavelength the data were collected at, and a program that takes *f′*/*f″* from -the file is given the right edge. The Bijvoet columns are present on any rotation merge, with or +and the wavelength, on a dataset of its own behind the reserved `HKL_base`, which is where the MTZ +format puts them. Older rugnux wrote the data on dataset 0, the id reserved for `HKL_base`, and +CCP4's `mtzinfo` then reported its 1.54187 Å (Cu Kα) default instead of the real wavelength — every +other reader tried, `mtzdmp`, `truncate`, `ctruncate`, gemmi, iotbx and `phenix.xtriage`, recovered +the true value from those files as well, so the effect was confined to that one report. Note that +`_unmerged.mtz` still reads 1.54187 under `mtzinfo` and is not wrong: its columns sit on +`HKL_base` deliberately, as POINTLESS expects, and the wavelength AIMLESS and POINTLESS read is the +per-batch one, which is correct. The Bijvoet columns are present on any rotation merge, with or without `-A`; a stills merge has no Bijvoet split and the file then stops after `F SIGF FreeR_flag`. There is deliberately **no `DANO`/`SIGDANO`** pair, the anomalous difference columns a CCP4 merged