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 <prefix>_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) <noreply@anthropic.com>
This commit is contained in:
2026-09-02 14:49:10 +02:00
co-authored by Claude Opus 5
parent 46c50ac744
commit 63a2f6744a
+8 -3
View File
@@ -58,9 +58,14 @@ H H H J Q K M K M F Q G L G L
```
`F` is the FrenchWilson 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
`<prefix>_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