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.
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
- If the molecule does not have structure diagram coordinates, they will be generated automatically according to the molecule's AtomCoordinates option.
- mol can be a Molecule object or something that can be easily converted to one, such as a systematic chemical name, a "Chemical" entity or ExternalIdentifier .
- Possible forms for patt include:
-
n the index of a particular atom{patt1,patt2,…} a list of patterns
- Patterns entered as Style [patt,spec]will be styled according to spec.
- MoleculePlot3D has the same options as Graphics3D , with the following additions and changes: [List of all options]
-
- Supported plot themes include:
-
"Spacefilling" atoms are depicted with spheres with radius matching the van der Waals radius"Tubes" atoms omitted"Wireframe" bonds rendered as lines
- Typical settings for PlotLegends include:
-
None no legendAutomatic automatically determine legend{lbl1,lbl2,…} use lbl1, lbl2, … as legend labels
- When patt is entered as an Association , the labeli will be used in the PlotLegends .
-
ImageMargins 0. the margins to leave around the graphicPreserveImageOptions Automatic whether to preserve image options when displaying new versions of the same graphicRotationAction "Fit" how to render after interactive rotation
List of all options
Examples
open all close allBasic 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 :
See Also
MoleculePlot Molecule AtomLabels AtomLabelStyle BondLabels BondLabelStyle BioMoleculePlot3D MoleculeMesh
Entity Types: Chemical Protein
Function Repository: MoleculeValuePlot3D MoleculeSymmetryPlot3D MoleculePrincipalMomentPlot MoleculeView BioSequenceMoleculePlot3D MoleculeMeshRegion
Related Guides
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: 18-November-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: 18-November-2025]}