I want to place a number on each atom (on a sphere) upon 3D plotting a molecule. For example, from:

mol = Molecule["h2co"]; MoleculePlot3D[m, {1, 2, 3, 4}, PlotLegends -> {"1", "2", "3", "4"}]

I get this:

enter image description here

But, this is not what I want. Instead of having this legend, I would like to have labels on the atoms themselves, like this:

enter image description here.

Any ideas on how to do this?


1 Answer 1

 mol = Molecule["Formaldehyde"];

You can use the option AtomLabels (Introduced in version 13.0):

MoleculePlot3D[mol, {1, 2, 3, 4}, 
 AtomLabels -> Thread[Placed[ {"1", "2", "3", "4"}, Center]],
 PlotLegends -> {"1", "2", "3", "4"}] 

enter image description here

Alternatively, you can construct a Graphics3D object using mol["AtomCoordinates"]["Magnitudes"] as Text positions and combine it with MoleculePlot[...] using Show:

    {Style[#, 16] & /@ Range[4], mol["AtomCoordinates"]["Magnitudes"]}]]] 

enter image description here


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