MoleculePlot3D

MoleculePlot3D[mol]

creates a three-dimensional model of the molecule mol.

MoleculePlot3D[mol,patt]

creates a model of mol where all atoms and bonds matching the pattern patt are highlighted.

Details and Options

Examples

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Basic Examples  (3)

Create a molecule and plot it in 3D:

Highlight the first and third atoms:

Highlight all oxygen atoms:

Highlight two different patterns:

Use different plot themes:

Scope  (2)

A pattern can match one or multiple positions in a molecule:

Highlight each carbonyl separately:

Highlight each carbonyl as a single color:

Highlight several patterns:

Options  (8)

AtomLabels  (1)

Label all atoms by their index:

Label only chlorine atoms by their index:

Label non-hydrogen atoms by their hybridization:

AtomLabelStyle  (1)

Set all labels to have the same style:

Set the label style depending on atom type:

BondLabels  (1)

Label all bonds by their index:

Label only bonds to chlorine atoms by their bond type:

BondLabelStyle  (1)

Give all bond labels the same style:

Label bonds differently based on their atoms:

ColorRules  (1)

Specify different colors for atomic elements:

IncludeHydrogens  (1)

By default, all hydrogen atoms are shown:

Show only the heavy atoms:

Create a molecule with only a few explicit hydrogens and show them in 3D:

PlotLegends  (1)

Use placeholders for plot legends:

Use the expressions to label the highlights:

PlotTheme  (1)

Use different plot themes to visualize a molecule in 3D:

Neat Examples  (1)

Combine a 3D molecule plot with a surface mesh using MoleculeMesh:

Wolfram Research (2019), MoleculePlot3D, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculePlot3D.html (updated 2021).

Text

Wolfram Research (2019), MoleculePlot3D, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculePlot3D.html (updated 2021).

CMS

Wolfram Language. 2019. "MoleculePlot3D." Wolfram Language & System Documentation Center. Wolfram Research. Last Modified 2021. https://reference.wolfram.com/language/ref/MoleculePlot3D.html.

APA

Wolfram Language. (2019). MoleculePlot3D. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/MoleculePlot3D.html

BibTeX

@misc{reference.wolfram_2025_moleculeplot3d, author="Wolfram Research", title="{MoleculePlot3D}", year="2021", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculePlot3D.html}", note=[Accessed: 08-July-2025 ]}

BibLaTeX

@online{reference.wolfram_2025_moleculeplot3d, organization={Wolfram Research}, title={MoleculePlot3D}, year={2021}, url={https://reference.wolfram.com/language/ref/MoleculePlot3D.html}, note=[Accessed: 08-July-2025 ]}