The joint post-refinement is asked twice, with the distance free and with it held at
the header. Where freeing it lowers the fit's held-out residual by more than that
residual's own standard error, the free fit is committed exactly as before. Where it
does not, the fit cannot tell - its own gain need not survive re-integration - so
both hypotheses are carried: the canonical pass runs at the free geometry as before
and once more at the header distance, and the run keeps the one whose RE-INTEGRATED
held-out residual is lower, the header's on a tie. The report says which
(POSTREFINE_DISTANCE_HELD), the pass decision names both realised residuals, and the
log prints the free fit's formal sd(distance) and its correlation with the cell
lengths, from the covariance of the solution.
Why: at a detector far enough away that no reflection reaches more than a few
degrees of 2theta, a longer distance and a larger cell move every spot the same way
to first order (the difference is of order sin^2 theta of the spot's position -
0.4 px rms per per cent over a 2M detector at 820 mm, against 2-3 px at usual
distances), so the fit finds a distance/cell pair that fits its own observations a
little better than the header, commits it, and the pass re-integrated there asks for
the next pair: a walk along the degenerate direction the realised residual never
ratifies. XDS leaves the distance out of IDXREF by default and its documentation
says to remove it from CORRECT where it drifts on low-resolution data; DIALS fixes
the wavelength for the same reason. Here the data are asked instead of a rule.
Measured: a sweep at 820 mm reaching 2theta ~ 9 deg no longer walks to 846 mm with
the cell 3.3 % too large (pool-B stopped it at 825.6 mm, still +1.1 %); it keeps
820 mm and its cell agrees with the reference at that distance to 0.2 %, R_meas
101 % -> 70 %, two passes fewer. 9yl4 keeps 600 mm (cell 0.5 % -> 0.1 % from the
deposition), 7mzt keeps 400 mm (R_meas 169 % -> 145 %, CC1/2 0.961 -> 0.986), 5lzl
keeps 689 mm on a tie (cell -0.3 % instead of +0.25 %, ISa 13.9 -> 11.6). Merged
output byte-identical on a lysozyme reference sweep at 110 mm (the free distance
wins its realised comparison), 8egn and 8pqd (decisive in-fit gains, no second arm)
and 8qq7 (the quality guard had already reverted it); one extra canonical pass
wherever the two arms are run.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT
leonarski_fandClaude Fable 5.1
36c24b6e5e
