"Analyze dataset" cleared the stored cell and space group unless "Use the stored
unit cell / space group" was ticked, and that checkbox defaulted off. But the
settings panel writes the user's own cell and space group onto the experiment, so
a cell typed into the panel was discarded too - while the checkbox label said
"stored", implying it came from the file.
It also contradicted the dialog next to it: "Refine geometry (stills)" is offered
and default-ticked precisely because a cell is present, and the run then removed
that cell. The default dialog state on a stills dataset with a known cell ran the
bundle adjustment with nothing to anchor on and dropped indexing off ffbidx, which
needs a cell, onto de-novo FFT.
Drop the checkbox and take the crystal from the panel, which already has exactly
the right semantics: "Unit cell known" ticked writes the cell and group, unticked
clears both, and a space group of 0 means none. So ticked = -C/-S, unticked =
bare rugnux, and what a run will use is always what is on screen. That also keeps
the copied command line honest, since RugnuxCommandLine emits -C/-S from the same
experiment. The panel is refilled from the file when one is opened, so a finished
job's _process.h5 becoming the active snapshot now shows its group and can be
cleared, instead of silently pinning every later run to it.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 5
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