Atom visualization settings
These options control the appearance of atoms in the 3D structure: geometry detail, material properties, ADP ring geometry, and the cutaway hatching used by the cutout-3d render style (the 2D hatch equivalents are plot2DStripeCount and plot2DStripeWidth under Rendering).
| Option | Type | Default | Description |
|---|---|---|---|
ellipsoidProbability | Number | 0.5 | Displayed probability for anisotropic displacement (ADP) ellipsoids, in (0, 1). The RMS ellipsoid is scaled by the chi-squared(3) quantile at this probability; 0.5 gives the conventional 50% probability ellipsoid. |
peanutScale | Number | 1.5381723183496745 | Positive visual multiplier for RMS displacement PEANUT radii. The surface radius is peanutScale × sqrt(nTUn) in Å; this is a display scale, not an enclosed probability. |
peanutMeridianCount | Number | 10 | Number of equally spaced meridian intervals drawn on PEANUT grid surfaces. |
peanutLatitudeIntervals | Number | 6 | Number of latitude intervals drawn from pole to pole on PEANUT grid surfaces. |
peanutGridPoleAxis | String | "structure-y" | Direction where PEANUT meridians converge. Use the structure Y axis for a common structure-fixed grid, or align each atom independently with one of its ordered principal displacement axes. |
peanutGridLineWidth | Number | 0.01 | Physical PEANUT grid-line width in Å for 3D cutout and 2D publication styles. |
atomDetail | Number | 3 | Level of detail for atom geometry (1–5). |
atomCutawayHysteresis | Number | 0.025 | Direction threshold that prevents cutaway octants flickering near an axis. |
atomCutawayStripeCount | Number | 7 | Number of hatch repeats across each cutaway disc. |
atomCutawayStripeWidth | Number | 0.5 | Atom-colour stripe width as a fraction of each repeat. |
atomColorRoughness | Number | 0.4 | Roughness of atom material (0–1). |
atomColorMetalness | Number | 0.5 | Metalness of atom material (0–1). |
atomADPRingWidthFactor | Number | 1 | Width factor for ADP (anisotropic displacement parameter) rings. |
atomADPRingHeight | Number | 0.06 | Height of ADP rings. |
atomADPRingSections | Number | 18 | Number of sections in ADP rings. |
atomADPInnerSections | Number | 7 | Number of inner sections in ADP rings. |
atomConstantRadiusMultiplier | Number | 0.25 | Multiplier for atom radius when using constant mode. |