leonarski_fandClaude Opus 5.5
093069be29
Three defects that stopped known-cell stills runs:
- The consensus cell compared every frame's cell to -C axis by axis. A run whose frames index in another
setting of the same lattice (axes in another order, another monoclinic choice) had no frame accepted, no
consensus cell and no output ("No crystal lattice was determined"), although it merged fine. A frame
whose lattice contains the given cell now counts on the given cell's axes (CellOnReference, the same
FindSublatticeBases the merge-stage relabel uses).
- The per-image ambiguity resolver relabelled a frame's reflections but left its lattice on the old axes.
Everything after it predicts from index and lattice: the sublattice relabel put such a frame through a
second transformation, and on a monoclinic cell with a near-symmetry (a+c nearly as long as a) the
merge came out at indices finer than anything measured, shells over 100% complete. The lattice now
follows the indices (ReindexLattice, B' = R^-1 B).
- With -C/-S the stills path replaced the known-cell indexer's lattice, already on the given axes, by
LatticeSearch's conventional choice, which on that near-symmetric cell is the other description on half
the frames. The indexer's lattice is now kept when it is close to the given cell.
Measured (cell + space group given, dimple against the deposited model and free set):
- monoclinic MbCO-type still set: was over-complete/broken with --model; now 2.06 A, R/Rfree 0.233/0.314
at 2.11 A (P1 merge before: 0.275/0.306).
- C-centred orthorhombic set: no MTZ before; now 3.27 A, R/Rfree 0.298/0.403 at 3.68 A (de novo 0.336/0.448).
- monoclinic two-form set, one form: cell P 1 21 1 with beta (was alpha); Rfree 0.310 -> 0.260, 3.05 -> 2.72 A.
- No change on seven other stills sets, nor on two rotation battery sets (5reo, lyso_x10sa_90deg_1).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Jungfraujoch
Application to receive and analyse data from the PSI JUNGFRAU and EIGER detectors, together with
rugnux, its program for processing stored diffraction data - rotation and serial, macromolecular
and small-molecule - from images to merged reflections.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.