Tour3DVideo

Visualization & Graphics
Life Sciences
Video Processing

Spiralling Around a Molecule

Use a piecewise function to create a helical path around a molecule for animation

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In this example, we will spiral around and fly-through the Clostridium perfringens epsilon toxin (6RB9), visualizing the protein molecule in 3D space.

Install the protein visualization paclet first:

In[1]:=

PacletInstall["WolframChemistry/ProteinVisualization"]

Out[1]=

PacletObject

Name: WolframChemistry/ProteinVisualization

Version: 1.2.2



Import and visualize the structure of the Clostridium perfringens epsilon toxin (6RB9) molecule:

In[2]:=

Needs["WolframChemistry`ProteinVisualization`"];testMol=ProteinBackboneAtomPlot"6RB9",

vizOptions



Out[2]=

	Chain A
	Chain B
	Chain C
	Chain D
	Chain E
	Chain F
	Chain G

Extract the underlying graphics structure:

In[3]:=

plot=ShowtestMol1,

vizOpts



Out[3]=

Define a set of functions to spiral around and fly through the molecule:

In[4]:=

center=Mean/@PlotRange[plot];radius=200;sphere[r_,center_][t_]:=rCos[2t]Sin

,Sin[2t]Sin

,Cos

+center;line[r_,center_][t_]:=With{tStart=4.5π,tEnd=5.5π},(sphere[r,center][0]-sphere[r,center][4π])

(t-tStart)

(tEnd-tStart)

+sphere[r,center][4π];positionFunction[t_]:=

sphere[radius,center][t]	0≤t<4π
sphere[radius,center][4π]	4π≤t<4.5π
line[radius,center][t]	4.5π≤t<5.5π
sphere[radius,center][0]	5.5π≤t≤6π

;

Observe the camera's path with respect to the molecule:

In[5]:=

ManipulateShowplot,ParametricPlot3DpositionFunction[t],{t,0,6π},

pltStyle

,Graphics3D

pointStyle

,Point[positionFunction[t]],

arrowStyle

,Arrow[{center,positionFunction[t]}],{t,0,6π},SaveDefinitionsTrue,ControlPlacementTop

Out[5]=

Generate the video tour:

In[6]:=

Parallelize@Tour3DVideoplot,t"CameraPosition"positionFunction[t],"SubjectPosition"center+{1,1,0},"ViewVertical"

viewVertical

[t],DefaultDuration6π

Out[6]=

External Links

Illuminating proteins: proteins, lighting, and videos, Anika Patel, Wolfram Community, STAFF PICKS, August 4, 2023

Related Symbols

Tour3DVideo

Publisher Information

Contributed by: Wolfram Staff

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This work is licensed under a Creative Commons Attribution 4.0 International License

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