The merged mmCIF carried the R-free flag in `_refln.status_free` as 1/0 and
wrote `o` into `_refln.status` on every row. `_refln.status_free` is not in the
PDBx/mmCIF dictionary - it is absent from mmcif_pdbx v4.0, v5.0, v5.288 and
v5.362, from CCP4's and phenix's shipped copies, and its wwPDB item page is a
404 - and no deposited structure-factor file uses it. `_refln.status` is the
item that carries the free set, with `f` for a test reflection and `o` for a
working one; on a deposition that also carries `_refln.pdbx_r_free_flag` the
two agree exactly.
Measured on a real merged file this run wrote:
CCP4 cif2mtz refuses the file outright - "Unexpected context type for
category REFLN" from its dictionary-validating parser, exit 1,
a 12-byte truncated MTZ. Dropping the non-dictionary column is
what fixes it: the same file without it converts.
gemmi converts, but its cif2mtz spec knows only `status` and
`pdbx_r_free_flag`, so FreeR_flag comes out 1 everywhere and
the free set is silently lost - R-free would then be computed
on the working set.
phenix worked, but only by a filename heuristic matching the words
"status" and "free".
Writing `f` while keeping the extra column is worse than either, because phenix
then finds two candidate free-set arrays and refuses the file, so the column
goes in the same change. After it, all three read the same 5% test set.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
leonarski_fandClaude Opus 5
7b1caa6ce5