Wolfram Function Repository

Instant-use add-on functions for the Wolfram Language

Function Repository Resource:

 MoleculeSymmetryPlot3D

Source Notebook

Show a molecule in 3D together with its symmetry elements

Contributed by: Jason Biggs

ResourceFunction["MoleculeSymmetryPlot3D"][mol]

returns a Manipulate combining a 3D plot of the Molecule mol together with graphical depictions of its symmetry elements.

Details and Options

Symmetry elements are displayed with the following Graphics3D primitives:
Tuberotation axes
Sphereinversion centers
Hyperplanereflection panes

Examples

Basic Examples (2) 

Tetramethyl ammonium has Td symmetry:

In[1]:=
m = Molecule["tetramethyl ammonium"]; m["PointGroupDisplay"]
Out[2]=

Visualize the symmetry elements present:

In[3]:=
ResourceFunction["MoleculeSymmetryPlot3D"][m]
Out[3]=

Visualize the C2 rotation axes in benzene:

In[4]:=
ResourceFunction["MoleculeSymmetryPlot3D"][Molecule@"Benzene"]
Out[4]=

Possible Issues (2) 

If a molecule's coordinates are not symmetric, no symmetry elements will be found:

In[5]:=
SeedRandom[12]; mol = Fold[ MoleculeModify[#1, {"SetBondLength", #2 -> RandomReal[{.9, 1.2}]}] &, Molecule["methane"], BondList[m1]]
Out[6]=
In[7]:=
ResourceFunction["MoleculeSymmetryPlot3D"][mol]
Out[7]=

Use the Merck molecular force field to find coordinates with higher symmetry:

In[8]:=
ResourceFunction["MoleculeSymmetryPlot3D"][ MoleculeModify[mol, "EnergyMinimizeAtomCoordinates"]]
Out[8]=

Publisher

JasonB

Version History

  • 1.0.0 – 05 August 2020

Related Resources

License Information