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WOLFRAM NOTEBOOK
Visualizing Molecules
Visualizing Molecules
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Molecules are not visible to the human eye so plots are needed to understand what is present.
2D plots are generated with the function.
Plot a water molecule:
water=MoleculePlot["water"]
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Plot a benzene molecule:
benzene=MoleculePlot["benzene"]
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Multiple plots can be combined with :
Show[water,benzene]
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Rotatable 3D molecule plots are generated with the function.
MoleculePlot3D["(2S)-N-[(1S)-2-carbamoyl-1-[[(2S)-1-[(2S)-2-[[(1S)-1-[[(1S)-1-carbamoyl-2-(4-methoxyphenyl)ethyl]carbamoyl]-4-(diaminomethylideneamino)butyl]carbamoyl]pyrrolidin-1-yl]-1-oxo-3-sulfanylidene-propan-2-yl]carbamoyl]ethyl]-2-[[(2S)-2-[[(2S)-3-(4-hydroxyphenyl)-2-[[2-(1-sulfanylcyclohexyl)acetyl]amino]propanoyl]amino]-3-phenyl-propanoyl]amino]pentanediamide"]
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Multiple 3D-representations of the same molecule are available:
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MapMoleculePlot3D,ImageSizeSmall,PlotTheme#&,{"Spacefilling","BallAndStick","Tubes","Wireframe"}
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The Wolfram Function Repository (WFR) function MoleculeView is a great way to see how 2D- and 3D-representations of the same molecule are related:
ResourceFunction["MoleculeView"]["5-fluoro-1-(2R,5S)-[2(hydroxymethyl)-1,3-oxathiolan-5-yl]cytosine"]
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When visualizing DNA, RNA or peptides, use the WFR functions BioSequenceMoleculePlot and BioSequenceMoleculePlot3D.
View the structure of the “beefy meaty peptide”:
ResourceFunction["BioSequenceMoleculePlot"][BioSequence["Peptide","KGDEESLA"]]
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View the three-dimensional structure of the “beefy meaty peptide”:
ResourceFunction["BioSequenceMoleculePlot3D"][BioSequence["Peptide","KGDEESLA"]]
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