-z (now also --reference; --reference-mtz still works) takes an SF-mmCIF
(e.g. a deposited -sf.cif, gzipped or not) as well as an MTZ. The format is
recognised by content: a file starting with "MTZ " is an MTZ, anything else
is parsed as CIF. The first merged reflection block with the requested
column (or, by default, one the auto choice accepts) is converted to a
gemmi::Mtz in memory with GEMMI's CifToMtz and then read by the unchanged
MTZ loader, so the in-memory reference is exactly what the MTZ path yields.
Unmerged (_diffrn_refln) and anomalous-only blocks are passed over; the log
names the block used.
The R-free set comes from _refln.status (f -> FreeR_flag 0, o -> 1: the
CCP4 convention the loader already reads) and is preferred to
_refln.pdbx_r_free_flag, whose convention varies by program; a status
column with no 'f' is ignored and pdbx_r_free_flag is used instead.
Checked on two open-arm sets in the deposited setting (one with F_meas_au
only, one with intensity_meas): reference loaded with the deposited cell and
group, the inherited free set agrees with the deposited status 'f' on every
common reflection, and the merge correlates at CC 0.99 with the deposition.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
