StructureMorph

Morph between two experimental structures of the same protein, moving residues along screw paths.

View source Guide and examplesInherits Animation

from proteinmotion import StructureMorph

Constructor

StructureMorph(
    source,
    target,
    *,
    align=None,
    chains=None,
    match=None,
    fade_out=(0.0, 0.35),
    fade_in=(0.65, 1.0),
    style='source',
    secondary='auto',
    easing='smooth',
)

Parameters

Parameter	Default	Description
`source`	Required	Structure shown before the morph.
`target`	Required	Structure that replaces the source at the end; chains, residues, ligands, and atoms may differ.
`align`keyword only	`None`	Region of the source whose matched Cα/C4′ atoms superpose the target; None uses the rigid core; False keeps the target where it is, for structures already superposed.
`chains`keyword only	`None`	Source-to-target chain ID mapping; None pairs chains automatically.
`match`keyword only	`None`	StructureMatch to reuse; None calls match_structures().
`fade_out`keyword only	`(0.0, 0.35)`	Interval of the clip, as fractions, in which source-only atoms fade out.
`fade_in`keyword only	`(0.65, 1.0)`	Interval of the clip, as fractions, in which target-only atoms fade in.
`style`keyword only	`'source'`	"source" gives the target the source's representation and colors; "target" keeps its own.
`secondary`keyword only	`'auto'`	"auto" blends residues whose DSSP state differs between the structures; "keep" leaves the cartoon unchanged.
`easing`keyword only	`'smooth'`	Easing of the whole morph.

Notes

Rigid domains rotate along arcs and keep their bond lengths; side chains turn through their χ angles; bond lengths then relax toward interpolated values. The path illustrates the difference between two endpoints, not a calculated pathway.

Example and output

Run this command from a repository checkout.

Code Render command

proteinmotion render examples/structure_morph.py HemoglobinMorph \
  -o hemoglobin-morph.mp4 --fps 60

Output Preview · 17.7 s · 60 fps

Hemoglobin from T to R

Deoxyhemoglobin (2DN2) morphs to oxyhemoglobin (2DN1, expanded to its tetramer), superposed on α1β1. α2β2 turns 14° in the image plane while O₂ appears at each heme. A heatmap shows Cα–Cα distances changing between the αβ dimers but not within them. The path illustrates the difference between the two structures.

Full source: HemoglobinMorph Download MP4

Methods and properties

Name	Description
targetsproperty	Objects whose state this animation changes.
resultproperty	The target structure, which replaces the source when the morph ends.
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.

targets

View source

StructureMorph.targets

Objects whose state this animation changes.

result

View source

StructureMorph.result

The target structure, which replaces the source when the morph ends.

bind()

View source

StructureMorph.bind()

Capture starting values when the scene schedules the animation.

Returns: None

Called by ProteinScene.play(). An animation instance can be bound once.

apply()

View source

StructureMorph.apply(alpha)

Evaluate the animation at eased progress alpha. Called by the timeline.

Parameter	Default	Description
`alpha`	Required	Eased animation progress in [0, 1].

Returns: None

during()

View source

Inherited from animation.Animation.

StructureMorph.during(seconds, *, delay=0)

Set this animation duration and start delay in seconds.

Parameter	Default	Description
`seconds`	Required	Positive animation duration in seconds.
`delay`keyword only	`0`	Nonnegative animation start delay in seconds.