SetTorsions

Animate backbone and side-chain torsions to new values in degrees; atoms rotate about bonds, so bond lengths and angles stay fixed.

View source Guide and examplesInherits Animation

from proteinmotion import SetTorsions

Constructor

SetTorsions(
    target,
    *,
    phi=None,
    psi=None,
    omega=None,
    chi1=None,
    chi2=None,
    chi3=None,
    chi4=None,
    chi5=None,
    conformation=None,
    anchor='center',
    secondary='auto',
    path='allowed',
    stagger=None,
    reverse=False,
    easing='smooth',
)

Parameters

Parameter	Default	Description
`target`	Required	Protein or Region whose amino acids change.
`phi`keyword only	`None`	φ, C(i−1)–N–Cα–C. Target angle in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged.
`psi`keyword only	`None`	ψ, N–Cα–C–N(i+1). Target angle in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged.
`omega`keyword only	`None`	ω, the peptide bond Cα–C–N(i+1)–Cα(i+1). Target angle in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged.
`chi1`keyword only	`None`	χ1 side-chain torsion. Target angle in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged.
`chi2`keyword only	`None`	χ2 side-chain torsion. Target angle in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged.
`chi3`keyword only	`None`	χ3 side-chain torsion. Target angle in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged.
`chi4`keyword only	`None`	χ4 side-chain torsion. Target angle in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged.
`chi5`keyword only	`None`	χ5 side-chain torsion. Target angle in degrees: one value for every selected residue, one per residue, or a {residue number: angle} dictionary. None leaves it unchanged.
`conformation`keyword only	`None`	Sets φ and ψ together: helix, alpha, 310, pi, strand, beta, parallel, antiparallel, ppii, extended, or left.
`anchor`keyword only	`'center'`	Part that stays still: "center" keeps the middle of each chain in place, "n" or "c" a terminus; a Region is held in place as a whole.
`secondary`keyword only	`'auto'`	"auto" blends the cartoon toward the DSSP assignment of the final conformation; "keep" leaves it unchanged.
`path`keyword only	`'allowed'`	"allowed" turns φ and ψ the way that keeps each residue in favored and allowed Ramachandran regions; "shortest" takes the smaller turn.
`stagger`keyword only	`None`	Fraction of the clip, in [0, 1), used to start residues one after another from N to C.
`reverse`keyword only	`False`	Stagger from C to N.
`easing`keyword only	`'smooth'`	Easing of each torsion's change.

Notes

Torsions in rings, such as proline φ, are skipped and listed by locked. Disulfides and ligands bonded to several residues stretch. The motion illustrates a change of angles, not a folding pathway.

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

"""Turn one ψ angle, then wind a whole peptide into an α helix.

A 12-residue alanine peptide is built as an extended β strand. ψ of Ala6 turns to
−45° with its atoms shown over the cartoon; then every residue moves to φ = −57°,
ψ = −47°, starting at the N terminus. DSSP assigns the helix from the final
coordinates, and the cartoon blends from coil to helix as the angles change.
"""

from proteinmotion import (
    FadeIn,
    Protein,
    ProteinScene,
    RamachandranPlot,
    SetTorsions,
    Text,
    Unwrite,
    Write,
)


class TorsionBasics(ProteinScene):
    def construct(self):
        peptide = Protein.build("AAAAAAAAAAAA", "strand").cartoon()
        middle = peptide.select(residues=6)
        middle.show_atoms()
        self.add(peptide)
        self.camera.frame(peptide, margin=1.0, aspect=self.width / self.height, screen_position=(0.32, 0.55))
        self.camera.phi = 0.3
        plot = RamachandranPlot(peptide, highlight=middle, position=(0.62, 0.14), size=(0.35, 0.7))
        self.add(Text("Torsion angles", font_size=48, font="semibold", position=(0.05, 0.07)))
        marker = middle.torsion_marker("psi", radius=1.6)
        self.play(FadeIn(plot), Write(marker), run_time=1.5)
        self.play(SetTorsions(middle, psi=-45, anchor="n"), run_time=2.5)
        self.play(Unwrite(marker), run_time=0.6)
        self.play(SetTorsions(peptide, conformation="helix", stagger=0.5), run_time=5)
        self.play(self.camera.animate.orbit(0.8), run_time=2.5)

Output Preview · 12.1 s · 60 fps

Torsion angles

A 12-residue alanine peptide: ψ of Ala6 turns, then every residue moves to α-helix angles.

Full source: TorsionBasics Download MP4

Methods and properties

Name	Description
lockedproperty	(residue index, torsion) pairs that could not rotate because they lie in rings.
bind()method	Capture starting values when the scene schedules the animation.
apply()method	Evaluate the animation at eased progress alpha. Called by the timeline.
during()method · inherited from Animation	Set this animation duration and start delay in seconds.
targetsproperty · inherited from Animation	Objects whose state this animation changes.