The pixels outside a CCD's active area, constant over the gain frames, are masked as dead before the run
starts. A CCD reads the deep shadow of a beam stop at one value too, so that mask took the shadow's
core, and the shadow finder - which reads only unmasked pixels and grows the shadow from where it is
deep - then found a fraction of it or nothing. Of the 48 open-arm CCD rotation sets, about half lost
most of their shadow: 9.35% -> 1.11% of the detector on PDB 3MEB, 10.79% -> 2.60% on 3R6O, 1.54% -> none
on 9UPT; the CCD stills sets lost theirs too. What went unmasked was the penumbra about the core, which is
not constant and was integrated as if exposed, and the shadow bit the integration's test of clipped
reflections reads. On 7BGU the background centre the finder draws its rings about moved 56 px.
The beam-stop step - the shadow finder and that centre - now reads the inactive pixels as the input has
them (ProcessConfig::inactive_pixels, passed by the CLI and the viewer where they mask them); everything
else keeps them masked as dead. On 11 CCD rotation sets the shadow is again exactly what it was before
the inactive mask, the mask's gain on 7BGU stays (d_min 2.42 A, R-free 0.190), 9UPT R-free 0.225 -> 0.219,
2WNN ISa 14.5 -> 15.4, 3MEB d_min 1.65 -> 1.56 A; the CCD stills sets get their shadow back (R-free within
0.001). Photon-counting sets are unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UqXYdL4qBGYRiSXSGXfCLu
leonarski_fandClaude Opus 5.5
c5fc3fa1d6