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New: colorblind-safe color toggle. It switches the chain colors to the Tol Muted palette (and back), and the axis gizmo, overhang shading and cavity-highlight colors to Okabe–Ito colors. Structures loaded while it's on start with the safe palette. A chain palette you picked yourself is kept; colors from an imported 3MF stay the file's own.
Fixed: a 3MF file that carries color only as slicer paint data (PrusaSlicer's slic3rpe:mmu_segmentation / Bambu-Orca's paint_color — e.g. files exported by ChimeraX's own 3MF exporter) imported as one flat gray color instead of its original per-part colors
Reworked ion/ligand handling: instead of one global "include ions & ligands" toggle, loading a PDB/mmCIF now shows a checklist of the heteroatoms actually present in that file, so you choose which ones to keep before the surface is built
Fixed: cavity sealing was skipping the large majority of detected voids as "too thin to seal," and got worse (not better) at higher resolution — sealing now erodes by a margin based on how far a cavity actually sits from the model's exterior, instead of one fixed margin for every cavity regardless of depth
The version badge now reads "v: 1.x.y" in the lower-right corner