leonarski_fandClaude Opus 5
574419dc6c
The Bravais class is chosen by a walk that reads two axes as EQUAL when they agree to a fixed relative tolerance, and the class carrying that equality is then imposed on everything below: the cell is refined with a = b, reflections are predicted from it, and they are integrated at those predicted positions. On a small cell the tolerance is far wider than the spot positions resolve, so a genuinely orthorhombic crystal whose a and b differ by 2 % is integrated as tetragonal and every decision downstream is read off the wreckage. Measure the equality instead of assuming it. The indexer already refines each candidate a second time with nothing held, so the first pass now reports how far that free refinement leaves the two axes apart. A relative split of eps displaces a reflection at radius r by eps/2 * r pixels: where that displacement at the far corner of the detector stays inside the integration disc, imposing the equality moves nothing out of its own box and the higher symmetry is kept with no extra pass. Where it does not, both hypotheses are run as probe-only passes - the promoted class, and the class the same walk carries when it is granted no length equality at all - and whichever realises the lower held-out positional residual is kept, the promoted class on a tie. Two small-molecule sets whose axes differ by 2 % now index, refine and merge in their own orthorhombic lattice instead of a tetragonal mean: one goes from a cell 1 % wrong and P 1 at CC1/2 0.19 to the deposited cell within 0.2 % and P 2 2 2 at CC1/2 0.95, the other from a tetragonal mean to a cell matching its reference to 0.4 %. Protein sets whose symmetry is real (P41212, P4222, I23, P6422, F4132) are unchanged: their free refinements leave the axes 0.02-0.10 % apart, a few tenths of a pixel, so the question is never asked. Where it was asked on a weak sweep whose free refinement diverged, the arms decided for the higher symmetry and the output was identical. No new threshold: the comparison is the integration radius the run already integrates at, and the arms are judged by HeldOutResidualFell, as the geometry walk's rounds are. postrefine_probe_only_ returns for the arms' sake - a pass run only to measure stops before the scaling engine is built, so neither arm pays for a merge or a space-group search. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT
Jungfraujoch
Application to receive data from the PSI JUNGFRAU and EIGER detectors.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.