leonarski_f and Claude Opus 5 7dc066c0f3
model: the placed coordinates carry the group they obey, not the data's ...
WritePlacedModel stamped the reflection files' space group on the placed
model unconditionally. That is right whenever the coordinates obey that
group - the ordinary case, and the subgroup case too, where the file just
holds more than one asymmetric unit of it - but wrong when the data were
merged in a supergroup of the model's group, or in the other hand. The
extra operations are then a claim the contents contradict: a refinement
program expands them, refines a structure that is not the model, and
reports nothing.
Measured on a public deposition whose data this run over-merged across a
pseudo-symmetry twofold: refining the written pair gave R-free 0.495,
where the same coordinates and the same reflections under the model's own
group give 0.285. The label alone was worth 0.21 of R-free.
The group is now taken from the argument only where every one of its
operations is one the model already has, and the model keeps its own
otherwise. The two files then disagree, which is the truth about them and
is warned about, rather than agreeing on something false.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com >
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leonarski_fandClaude Opus 5
7dc066c0f3