writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does

The placed-model END block lost everything but the atoms, so the writer's _model.cif had no sequence
references, authors, software or secondary structure, and gemmi relabelled the subchains. The block now
also carries label_asym_id, label_entity_id and label_seq_id per atom and the input model's metadata as the
mmCIF categories gemmi writes without coordinates (metadata_mmcif), which the writer parses with gemmi and
puts back. The writer's _model.cif is now the same text as the one rugnux writes itself and as
/rugnux/model.cif serves. Older blocks without the new fields are read as before.

Test: a predicted myoglobin model through END -> CBOR -> writer gives byte-identical _model.cif/_model.pdb
to WritePlacedModel and to PlacedModelMmcif, with its _struct_ref, _entity_poly_seq, _audit_author,
_software and _struct_conf.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 29d752e6a107e3b8bc71ad6e9af0d81064966537)
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leonarski_f committed 2026-10-22 20:18:51 +02:00
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@@ -4164,9 +4164,9 @@ Name | Type | Description | Notes
Get the model as placed by the last rugnux live run
The model placed against the data by molecular replacement or validation, as mmCIF: the coordinates, cell
and space group of the `_model.cif` file written beside the data, with the input model's own metadata
(entities, citation) kept. Kept as long as `/rugnux/status`.
The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
`_model.cif` file written beside the data: the data's cell and space group, with the input model's own
metadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.
### Example