MoleculeMesh

MoleculeMesh[mol]

returns a BoundaryMeshRegion object representing the Molecule or BioMolecule mol.

MoleculeMesh[mol,type]

returns a mesh of surface type type.

MoleculeMesh[mol,{type,param1val1,…}]

uses the supplied parameters to create the mesh.

Details and Options

  • Supported mesh types include
  • "Gaussian"Gaussian surface
    "VanDerWaals"Van der Waals surface
    "SolventAccessible"solvent accessible surface
    "BallAndStick"spheres for atoms and cylinders for bonds
  • The "VanDerWaals" surface is a union of spheres for each atom using its van der Waals radius.
  • A Gaussian surface is defined as an isosurface of the scalar field defined by , where xi and ri are the position and radius of the i^(th) atom, respectively, and d is a prefactor. The "Gaussian" surface has the following parameters and default values:
  • "GaussianPrefactor"0.9the parameter d
    "Isosurface"1.1the value of the isosurface
  • The "SolventAccessible" surface has the following parameters and default values:
  • "ProbeRadius"1.4an atom radius that is added to each atom in the molecule
  • MoleculeMesh has the following options:
  • MaxCellMeasure Automaticmax cell measure
    IncludeWaters Falsewhether to include waters of hydration
    IncludeHydrogensAutomaticwhether to include hydrogen atoms
  • SurfaceArea and Volume will act on a molecule mesh to return the surface are and volume as real numbers, with units of Angstroms2 and Angstroms3, respectively.

Examples

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Basic Examples  (2)

Convert a molecule to a boundary mesh:

Create a mesh for the Gaussian surface of this molecule:

Convert a biomolecule to a boundary mesh:

Scope  (3)

Create a mesh region showing the atoms and bonds as spheres and tubes:

Show the same molecule with no bonds and atoms represented as spheres with their van der Waals radii:

Use different parameter settings for the "Gaussian" surface:

Combine a Gaussian mesh with a ribbon diagram from BioMoleculePlot3D to show the ribbons in place:

Options  (2)

IncludeWaters  (1)

Some biomolecules have extra water molecules taken from the crystal structure. These typically have no hydrogens attached. By default, these are not included in a MoleculeMesh output. Use the option IncludeWatersTrue to show the waters:

MaxCellMeasure  (1)

Use the option MaxCellMeasure to control the mesh quality:

Neat Examples  (2)

Start with two different conformers for a metacyclophane molecule:

View the ball-and-stick mesh regions:

Create Gaussian surfaces for these conformers:

Find the surface area and volume:

Find the isomers of decane with the smallest and largest surface areas:

A greater degree of branching leads to a decrease in the surface area:

Create a scatter plot of the volume versus surface area for these isomers:

Wolfram Research (2025), MoleculeMesh, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeMesh.html.

Text

Wolfram Research (2025), MoleculeMesh, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeMesh.html.

CMS

Wolfram Language. 2025. "MoleculeMesh." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/MoleculeMesh.html.

APA

Wolfram Language. (2025). MoleculeMesh. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/MoleculeMesh.html

BibTeX

@misc{reference.wolfram_2024_moleculemesh, author="Wolfram Research", title="{MoleculeMesh}", year="2025", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculeMesh.html}", note=[Accessed: 15-January-2025 ]}

BibLaTeX

@online{reference.wolfram_2024_moleculemesh, organization={Wolfram Research}, title={MoleculeMesh}, year={2025}, url={https://reference.wolfram.com/language/ref/MoleculeMesh.html}, note=[Accessed: 15-January-2025 ]}