Creating a Python tool for visualizing molecular structures in chemistry involves writing a program that generates three-dimensional representations of molecules. Here, we will use the RDKit, matplotlib, and mpl_toolkits libraries.

Below are the steps you need to follow.

Step 1: Installation:

Firstly, we need to install these libraries. Open your terminal or command prompt and type:

pip install rdkit matplotlib

This will install both RDKit and matplotlib. mpl_toolkits is usually installed with matplotlib.

Step 2: Importing required Libraries:

Here is how you can import these libraries in your python code.

import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw

Step 3: Loading a Molecule:

You can load a molecule in your program through the use of Simplified Molecular Input Line Entry System (SMILES) notation, or by importing a file that describes your molecule.

molecule = Chem.MolFromSmiles('C1CCCCC1') # example of cyclohexane

Step 4: Extracting the 3D Coordinates:

RDKit will automatically generate 3D coordinates for your molecule, which you can then extract and store in a variable:

coordinates = molecule.GetConformer().GetPositions()

Step 5: Drawing the Molecule:

Finally, we can use matplotlib to draw our molecule. We’ll draw each atom as a scatter point and each bond as a line between two points.

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')

for atom_index_1 in range(molecule.GetNumAtoms()):
    atom_1 = molecule.GetAtomWithIdx(atom_index_1)
    for atom_index_2 in range(atom_index_1 + 1, molecule.GetNumAtoms()):
        atom_2 = molecule.GetAtomWithIdx(atom_index_2)
        # Check if atom_1 and atom_2 are bonded
        if molecule.GetBondBetweenAtoms(atom_index_1, atom_index_2):
            ax.plot([coordinates[atom_index_1][0], 
                     coordinates[atom_index_2][0]], 
                    [coordinates[atom_index_1][1], 
                     coordinates[atom_index_2][1]],
                    [coordinates[atom_index_1][2], 
                     coordinates[atom_index_2][2]],
                    color='black')
        ax.scatter(coordinates[:, 0], coordinates[:, 1], coordinates[:, 2],
                   alpha=0.6, edgecolors='w', s=80)
        ax.set_xlabel('X')
        ax.set_ylabel('Y')
        ax.set_zlabel('Z')
        plt.show()

With this simple Python tool, you can visualize the structure of molecules in 2D and 3D. It will be a beneficial tool in the chemistry field for visualizing different molecular structures. Note that this tool works best for small to medium-sized molecules, as large molecules may take a long time to plot and may result in an image that is difficult to interpret.

Remember this is a basic example. Depending on the complexity of the molecules you are trying to create, you might need more advanced libraries or more in-depth code.