RegionHighlight

Draw a sphere, wire box, or atom halos around a region.

View source Guide and examplesInherits Protein

from proteinmotion import RegionHighlight

Constructor

RegionHighlight(
    region,
    *,
    style='sphere',
    color='#f2ba67',
    opacity=None,
    padding=None,
    line_width=0.12,
)

Parameters

Parameter	Default	Description
`region`	Required	Region selection attached to a protein.
`style`keyword only	`'sphere'`	"sphere", "box", or "atoms".
`color`keyword only	`'#f2ba67'`	Hex color or RGB values. For tint setters, None restores the representation’s base palette.
`opacity`keyword only	`None`	Opacity in [0, 1]. None uses 0.9 for a box and 0.18 otherwise.
`padding`keyword only	`None`	Extra size in ångströms. None uses 0.3 for atoms and 2.0 otherwise.
`line_width`keyword only	`0.12`	Box edge radius in ångströms.

Notes

The highlight follows the region’s coordinates and parent transform. Animate its opacity; apply movement to the parent protein. Highlight geometry describes a region boundary.

Example and output

This excerpt runs inside a scene’s construct() method. The full example file includes imports, structure loading, and camera setup. Run it from a repository checkout.

Code Scene excerpt

p = ubiquitin()
frame(self, p)
helix = p.select(residues=(23, 34))
for style in ("sphere", "box", "atoms"):
    marker = helix.highlight(
        style=style,
        color="#f2ba67",
        padding=1.0,
        opacity=0.3,
    )
    self.play(FadeIn(marker), run_time=0.6)
    self.wait(1.2)
    self.play(FadeOut(marker), run_time=0.6)

Output Preview · 7.2 s · 60 fps

3D highlights

Sphere, box, and atom highlights on the same helix.

Full source: HighlightStyles Download MP4

Methods and properties

Name	Description
copy()method	Create another region.highlight() for independent styling. Calling copy() raises ValueError.
select()method · inherited from Protein	Select atoms by author chain, residue number, and atom name.
label_residues()method · inherited from Protein	Create labels for the selected residues. Extra options go to ResidueLabels.
hydrogen_bonds()method · inherited from Protein	Create a hydrogen-bond analysis. Options go to HydrogenBonds.
electrostatics()method · inherited from Protein	Create a screened Coulomb analysis. Options go to Electrostatics.
from_file()class method · inherited from Protein	Load PDB or mmCIF coordinates and retain all models with matching atom identities.
from_trajectory()class method · inherited from Protein	Create a protein from the trajectory’s topology and first frame.
positionsproperty · inherited from Protein	Current atom coordinates in the protein’s local coordinate frame.
atom_progressproperty · inherited from Protein	Current interpolation fraction for each atom.
atom_opacitiesproperty · inherited from Protein	Current per-atom opacity, including global opacity and residue fades.
set_positions()method · inherited from Protein	Replace coordinates while preserving atom identities and topology.
center()method · inherited from Protein	Move the molecular centroid to the world origin.
shift()method · inherited from Protein	Translate the object by an offset.
rotate()method · inherited from Protein	Rotate around the molecular centroid.
scale()method · inherited from Protein	Scale around the molecular centroid.
set_opacity()method · inherited from Protein	Set or animate opacity in [0, 1].
set_color()method · inherited from Protein	Apply a tint across all representations. None restores the base palette.
color_by()method · inherited from Protein	Apply residue property colors and optional cartoon thickness before adding the protein to a scene.
color_residues()method · inherited from Protein	Apply a tint to the selected residues in every representation.
set_residue_opacity()method · inherited from Protein	Set opacity on the selected residues.
surface()method · inherited from Protein	Show a van der Waals, solvent-accessible, or voxel solvent-excluded surface.
cartoon()method · inherited from Protein	Show helices, sheet arrows, and coils as a cartoon.
ribbon()method · inherited from Protein	Show a continuous backbone ribbon.
ball_and_stick()method · inherited from Protein	Show element-colored atom spheres and covalent bond cylinders.
with_secondary_structure()method · inherited from Protein	Assign helix, sheet, and coil labels before adding the protein to a scene.
animateproperty · inherited from Protein	Create a builder for protein transforms, opacity, and color animation.
model_matrixproperty · inherited from Protein	Current 4 × 4 transform from local to world coordinates.
snapshot()method · inherited from Protein	Capture the current state for deterministic timeline evaluation.
restore()method · inherited from Protein	Restore a state produced by snapshot().

Parameter	Default	Description
`chain`keyword only	`None`	Author chain ID or a collection of IDs; None selects all chains.
`residues`keyword only	`None`	Author residue number, inclusive (first, last) tuple, or list of individual numbers.
`atoms`keyword only	`None`	Atom name or list of names, such as "CA"; None selects all atom names.

Parameter	Default	Description
`charges`	`'formal'`	"formal" side-chain templates or one charge per atom, in elementary charge units.
`**kwargs`	—	Additional keyword options described below or in the linked constructor.

Parameter	Default	Description
`path`	Required	Input or output file path, as specified by the operation.
`**kwargs`	—	Additional keyword options described below or in the linked constructor.

Parameter	Default	Description
`angle`	Required	Rotation angle in radians.
`axis`	`(0, 1, 0)`	Nonzero 3D rotation axis; it is normalized internally.

Parameter	Default	Description
`values`	Required	Numerical input values; see the shape and missing-value rules for this object.
`scale`keyword only	`None`	ColorScale shared by the structure, plots, and legend. None derives limits from finite values.
`thickness`keyword only	`None`	Optional (minimum, maximum) positive cartoon cross-section scale factors. Missing values use 1.

Parameter	Default	Description
`color`	Required	Hex color or RGB values. For tint setters, None restores the representation’s base palette.
`chain`keyword only	`None`	Author chain ID or a collection of IDs; None selects all chains.
`residues`keyword only	`None`	Author residue number, inclusive (first, last) tuple, or list of individual numbers.

Parameter	Default	Description
`opacity`	Required	Opacity in [0, 1], from transparent to opaque.
`chain`keyword only	`None`	Author chain ID or a collection of IDs; None selects all chains.
`residues`keyword only	`None`	Author residue number, inclusive (first, last) tuple, or list of individual numbers.

Parameter	Default	Description
`kind`keyword only	`'ses'`	Surface type: "vdw", "sas", or "ses".
`probe_radius`keyword only	`1.4`	Solvent probe radius in ångströms.
`resolution`keyword only	`0.7`	Surface grid spacing in ångströms; smaller values increase detail and cost.
`color`keyword only	`'secondary'`	Base palette: "secondary", "rainbow", "chain", or a fixed color.
`update`keyword only	`'rebuild'`	"rebuild" recalculates the surface as coordinates change; "deform" moves the reference mesh.
`**kwargs`	—	Additional keyword options described below or in the linked constructor.

Parameter	Default	Description
`color`keyword only	`'rainbow'`	Base palette: "secondary", "rainbow", "chain", or a fixed color.
`width`keyword only	`1.05`	Ribbon width in ångströms.

Parameter	Default	Description
`atom_scale`keyword only	`0.3`	Multiplier applied to element van der Waals radii for ball-and-stick atoms.
`bond_radius`keyword only	`0.14`	Covalent bond cylinder radius in ångströms.