ColorByProperty

Animate property-based residue colors and optional cartoon thickness.

from proteinmotion import ColorByProperty

Constructor

ColorByProperty(
    protein,
    values,
    *,
    scale=None,
    thickness=None,
    residue_delay=0,
    reverse=False,
    easing='smooth',
)

Parameters

Parameter	Default	Description
`protein`	Required	Protein object to read or animate.
`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.
`residue_delay`keyword only	`0`	Delay in seconds between successive residue starts.
`reverse`keyword only	`False`	Reverse residue or glyph order.
`easing`keyword only	`'smooth'`	Per-residue interpolation: "smooth" or "linear".

Notes

Residue delays are in seconds. run_time must exceed total delay. The scale remains fixed during the transition.

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 Full script

"""Map 1UBQ Cα B factors to residue color and cartoon thickness."""

from pathlib import Path

from proteinmotion import (
    ColorByProperty,
    ColorLegend,
    ColorScale,
    Protein,
    ProteinScene,
    Representation,
    ResidueValues,
    Rotate,
    Text,
)

DATA = Path(__file__).parent / "data"


class NumericalProperties(ProteinScene):
    def construct(self):
        protein = Protein.from_file(DATA / "1ubq.cif").center()
        values = ResidueValues.b_factors(protein)
        scale = ColorScale(0, 40)
        self.add(protein)
        self.camera.frame(protein, margin=1.08)
        self.add(Text("Residue properties", position=(0.06, 0.07), font_size=42))
        self.add(Text("Ubiquitin · Cα B factors", position=(0.06, 0.13), font_size=25))
        self.add(ColorLegend(scale, title="B factor", unit="Å²", position=(0.06, 0.8)))
        self.play(
            ColorByProperty(protein, values, scale=scale, thickness=(0.6, 1.8), residue_delay=0.012),
            Rotate(protein, 0.25),
            run_time=2.5,
        )
        self.wait(0.5)
        self.play(Representation(protein, "ball_and_stick"), run_time=1.5)
        self.play(Rotate(protein, 0.3), run_time=1)
        self.play(Representation(protein, "surface"), run_time=1.5)
        self.play(Rotate(protein, 0.25), run_time=1.5)

Output Preview · 8.5 s · 60 fps

B factors across representations

1UBQ B factors control residue color and cartoon thickness.

Full source: NumericalProperties Download MP4

Methods and properties

Name	Description
bind()method	Capture starting values when the scene schedules the animation.
apply()method	Evaluate the animation at eased progress alpha. Called by the timeline.
targetsproperty · inherited from Animation	Objects whose state this animation changes.