# Representing vertices as spheres in Graphics 3D [closed]

I'm representing a portion of molecule, P3HT, in Mathematica as a pentagon that I build using Polygon and Graphics3D.

I would like to represent the vertices of the pentagon as spheres(corresponding to atoms).

If possible I would like to add a vector perpendicular to the P3HT plane stemming from the centroid of the plane.

Here's what I have so far:

The atomic coordinates:

C1 := {-1.51767 , 2.46541, -0.0036}
C2 := {-1.15943, 1.11229, -0.00326}
C3 := {0.25701, 0.88881, -0.00082}
C4 := {0.9979, 2.09239, 0.00071}
S := {-0.10561, 3.33212, -0.00095}


The molecular plane, defined by the atomic coordinates:

P3HTPlane = Polygon[{{-1.51767, 2.46541, -0.0036}, {-1.15943,
1.11229, -0.00326}, {0.25701, 0.88881, -0.00082}, {0.9979,
2.09239, 0.00071}, {-0.10561, 3.33212, -0.00095}}]


The centroid of the plane:

OO = RegionCentroid[P3HTPlane]


The plot of the plane with the centroid included:

Graphics3D[{LightOrange, P3HTPlane, Red, PointSize[0.02], Point[OO]},
BoxRatios -> {1, 1, 1}]


In case it helps, here's the molecule I'm working with:

ChemicalData["3-hexylthiophene", "MoleculePlot"]


Thanks for the help!

• You can draw a sphere centered at C1 with radius say 0.1 using Sphere[C1, 0.1]. You can draw multiple spheres using Sphere[C1, 0.1], Sphere[C2, 0.1], ... or just Sphere[{C1, C2, ...}, 0.1] for short. You'll want to remove the BoxRatios -> {1, 1, 1}` option though or the spheres won't look like spheres. – Rahul Aug 26 '16 at 23:12
• Awesome! I got the whole thing working. Thank you very much! – Victor Murcia Aug 26 '16 at 23:57