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Merged mmCIF: drop the scaled unmerged block

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The unmerged observations already leave a run as the unmerged MTZ (and
the scaled fulls as the .hkl), and deposition does not come straight
from rugnux, so the _diffrn_refln block made the .cif up to ten times
larger for no consumer. The .cif is one data block again; the keys,
software rows, metadata, R_merge/R_pim/CC* and provenance stay.
ScaledFull loses the scale and frame it carried only for that block.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
This commit is contained in:
leonarski_f
2026-10-09 18:51:56 +02:00
co-authored by Claude Opus 5.5
parent 5584460de0
commit 4120b0daa8
6 changed files with 21 additions and 115 deletions
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tests/WriteReflectionsTest.cpp
+3 -21
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@@ -232,7 +232,7 @@ TEST_CASE("CC* from CC1/2", "[write_reflections][portable]") {
CHECK(std::isnan(CCStar(NAN)));
}
TEST_CASE("Merged mmCIF: PDBx keys, merging R-factors and the scaled unmerged block",
TEST_CASE("Merged mmCIF: PDBx keys, merging R-factors and provenance",
"[write_reflections][portable]") {
jfjoch_test::SyntheticMergeParams params;
params.true_space_group = "P 43 21 2";
@@ -254,12 +254,6 @@ TEST_CASE("Merged mmCIF: PDBx keys, merging R-factors and the scaled unmerged bl
statistics.shells = {shell};
statistics.overall = shell;
// Three fulls, one without a usable sigma - that one is left out, as from the .hkl.
const std::vector<ScaledFull> fulls{
{1, 2, 3, 200.0f, 20.0f, 1.25f, 0.4f},
{-1, -2, -3, 100.0f, 12.0f, 0.8f, 9.6f},
{4, 5, 6, 10.0f, 0.0f, 1.0f, 3.0f},
};
OutputProvenance provenance;
provenance.collection_date = "2026-07-13T13:48:52.413Z";
provenance.command_line = "rugnux -o 'my run' /data/x_master.h5";
@@ -268,11 +262,11 @@ TEST_CASE("Merged mmCIF: PDBx keys, merging R-factors and the scaled unmerged bl
const auto path = (std::filesystem::temp_directory_path() / "rugnux_merged_test.cif").string();
WriteMmcifReflections(reflections, TETRAGONAL_CELL, experiment, statistics, ErrorModelReport{},
TwinningAnalysisResult{}, fulls, provenance, path, 2);
TwinningAnalysisResult{}, provenance, path, 2);
gemmi::cif::Document doc = gemmi::read_cif_gz(path);
std::filesystem::remove(path);
REQUIRE(doc.blocks.size() == 2);
REQUIRE(doc.blocks.size() == 1);
gemmi::cif::Block &merged = doc.blocks[0];
CHECK(merged.name == "sample");
CHECK(*merged.find_value("_reflns.pdbx_ordinal") == "1");
@@ -301,18 +295,6 @@ TEST_CASE("Merged mmCIF: PDBx keys, merging R-factors and the scaled unmerged bl
CHECK(shells[0][1] == "0.0500");
CHECK(shells[0][2] == "0.0300");
gemmi::cif::Block &unmerged = doc.blocks[1];
CHECK(unmerged.name == "sample_unmerged");
gemmi::cif::Table obs = unmerged.find("_diffrn_refln.", {"id", "pdbx_image_id", "index_h",
"intensity_net", "intensity_sigma",
"pdbx_scale_value"});
REQUIRE(obs.length() == 2);
CHECK(obs[0][0] == "1");
CHECK(obs[0][1] == "1"); // peaks on frame 0.4 -> image 1
CHECK(obs[1][1] == "11"); // 9.6 -> image 11
CHECK(obs[1][2] == "-1");
CHECK(gemmi::cif::as_number(obs[0][3]) == Catch::Approx(200.0));
CHECK(gemmi::cif::as_number(obs[1][5]) == Catch::Approx(0.8));
}
TEST_CASE("MTZ history: command line and input, in records of at most 80 characters",