`--model` re-fractionalizes the model into the data cell and then places it as
one rigid body, but the placed coordinates never reached disk. On a lysozyme
sweep against a non-isomorphous deposited model the move is 3.058 deg and
1.035 A, so a user overlaying their input model on rugnux's maps was out by
exactly that, and no file on disk corresponded to the maps at all.
`<prefix>_model.cif` is that file: the input's chains, residues, ligands,
waters, B-factors, occupancies and anisotropic Us, at the coordinates the maps
were computed from. `<prefix>.cif` is already the merged reflections, hence the
suffix.
The cell and space group come from the same two values WriteReflections is
given - the unit cell and DiffractionExperiment::GetSpaceGroupOrP1() after
AdoptModelFrame has settled the enantiomorph - so the coordinate file and the
.mtz beside it always agree. Taking them from the input model would not: with
data merged in P4(1)2(1)2 and a P4(3)2(1)2 model, the written reflections take
the model's group, which is neither the data's original label nor, when the
model is rejected, the model's own.
Written whenever the maps are, not only where the rigid-body step was
committed. The model is re-fractionalized and may be relabelled whatever the
placement decided, so an unmoved model is still not the input file; and a model
the null rejected is scored, placed and mapped like any other - the negative
result, and the case where the density is most worth looking at.
Nothing in the tree could write coordinates: gemmi_gph declared to_mmcif.hpp
but src/to_mmcif.cpp had been trimmed from the vendored subset. Both it and
to_pdb.cpp (to_mmcif.cpp calls its use_hetatm) are vendored from the same
gemmi 0.7.5 the rest of gemmi_gph comes from, unmodified, and every header they
include was already there. Same package, same MPL-2.0, same LICENSE.txt already
collected into licenses/gemmi.txt and already listed against `gemmi_gph/` in
THIRD_PARTY_NOTICES.md, so no new row and no new licence text.
Verified end to end: read back with gemmi the file differs from the
re-fractionalized input by exactly the reported 3.058 deg / 1.035 A with 0.0000 A
rms about that rigid move, and REFMAC5 at zero cycles against rugnux's own .mtz
starts at R-free 0.3667 where rugnux reports 0.3826 - against 0.5832 for the
unplaced input model, where rugnux reports 0.5911 before the placement.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
leonarski_fandClaude Opus 5
28a58e94b9
