- ModelValidation reads the model and, where it carries non-given NCS operators
(_struct_ncs_oper 'generate' / MTRIX without the given flag), expands them
(gemmi expand_ncs, vendored assembly.cpp from GEMMI 0.7.5, MPL-2.0 as the rest
of gemmi_gph). Same in the battery's model_check.py and depdata_check.py.
An icosahedral-virus entry deposited as 3 of the 45 chains of its ASU was
scored against a fifteenth of its atoms: R-free 0.545 -> 0.297.
- The indexing the model chooses (AdoptModelFrame) now moves the cell with the
indices (reseat_integrated in the main path; CellInBasis in the forecast,
twin-file and stills/scale paths). A near-symmetry law (b within 2% of c, beta
a degree off 90, a~b in P1) relabelled the reflections only, so the files were
written with two axes swapped or beta flipped relative to the indices. Where
the law moved the cell, the validation is remade on the moved cell.
Measured on 18 open/in-house sets with models: p.hkl and MTZ reflection data
bit-identical on all; cell and model R unchanged where the law is exact; the
cell now matches the deposited one on the 6 pseudo-merohedral cases (orthorhombic
a/c swap, three monoclinic beta flips, a P1 alpha/beta swap), R-free within
+-0.001 there.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3
leonarski_fandClaude Opus 5.5
1f27fba1f3