leonarski_f
2ba28aea0e
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PixelRefine's reference can now be a merged/observed-intensity MTZ, not only a calculated F-model. If F-model is missing, read a mean-intensity column (IMEAN, which a jfjoch merge writes; also I/IOBS/Iobs/I-obs, or any 'J'-type column) and use it directly as I_ref (F-model is squared, intensities are not). This enables a SELF-SEEDED / EM-style workflow: run a first pass (traditional integration, or PixelRefine against an external reference) to produce a merge, then re-run PixelRefine with `-z <that merge>.mtz` so it scales against the data's own intensities - free of the reference structure's non-isomorphism bias - and iterate. Verified: a jfjoch IMEAN merge loads as the reference and PixelRefine runs against it (crystal 2, 55279 reflections, CC1/2 94.3). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>