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docs: worked Phaser and SHELX routes, and the MTZ base dataset they need

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Both programs were run on merged rugnux output and the commands are the ones
that worked, error messages included.

Phaser takes myrun.mtz with no LABIN, picking IMEAN/SIGIMEAN and the cell,
group and resolution out of the file; MODE MR_AUTO already searches both hands
of an enantiomorphic pair and returned the hand opposite the one in the header
on a tetragonal test. SGALTERNATIVE SELECT ALL covers the screw variants the
report lists as indistinguishable, MODE CCA prints the list without searching,
and a wrong point group has to be re-merged instead. mmCIF is refused by 2.8.3
in both the CCP4 and the phenix build; gemmi cif2mtz gives the same solution.

SHELXC reads only myrun.hkl - it refuses an MTZ and exits 0 while doing it -
and needs CELL and SPAG repeated, since HKLF 4 carries no metadata. A default
rotation merge already writes the Bijvoet split, so no flag is needed and
--no-export-unmerged hides nothing. On a 5 keV cubic sweep SHELXD separated a
space-group pair the merged intensities could not (CFOM 69.4 against 52.0) and
SHELXE solved it, 42.9 % against 15.3 % autotrace CC between the two hands; a
tetragonal sweep at lower completeness and multiplicity did not separate at
all, and that is recorded too.

Verifying it exposed one defect. The merged MTZ was written with its data
dataset at id 0, the id MTZ reserves for HKL_base, so mtzlib dropped the
wavelength and mtzinfo reported the 1.54187 A default - the wrong edge for
anything taking f'/f'' from the file. Writing HKL_base first, as the unmerged
writer already does, puts the real wavelength back; Phaser's solution is
unchanged either way.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
This commit is contained in:
leonarski_f
2026-09-02 13:07:03 +02:00
co-authored by Claude Opus 5
parent 6b738713e8
commit d5cf3a6e58
3 changed files with 202 additions and 10 deletions
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image_analysis/WriteReflections.cpp
+5 -4
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@@ -451,7 +451,11 @@ void WriteMtzReflections(const std::vector<MergedReflection> &reflections,
mtz.title = "Rugnux merged reflections";
mtz.history.push_back("From Rugnux " + jfjoch_version() + ", data reduction");
// Add dataset
// Add dataset. HKL_base first, so the data dataset is id 1: a dataset written as id 0 is the
// reserved base dataset as far as CCP4's mtzlib is concerned, and the wavelength on it is
// dropped - mtzinfo then reports the Cu K-alpha default 1.54187 A, which is what a program that
// takes f'/f'' from the file would phase on.
mtz.add_base(); // the HKL_base dataset and the H K L columns
gemmi::Mtz::Dataset& ds = mtz.add_dataset("native");
ds.crystal_name = experiment.GetSampleName();
ds.wavelength = experiment.GetWavelength_A();
@@ -463,9 +467,6 @@ void WriteMtzReflections(const std::vector<MergedReflection> &reflections,
bool has_anom = true;
const std::vector<MergedOutRow> out_rows = BuildMergedRows(reflections, experiment, has_anom);
mtz.add_column("H", 'H', dataset_id, -1, false);
mtz.add_column("K", 'H', dataset_id, -1, false);
mtz.add_column("L", 'H', dataset_id, -1, false);
mtz.add_column("IMEAN", 'J', dataset_id, -1, false);
mtz.add_column("SIGIMEAN", 'Q', dataset_id, -1, false);
if (has_anom) {