Small Molecules

small molecule graphics
In ChemDoodle 3D, you have powerful tools for working with atoms and bonds. The above image was rendered in ChemDoodle 3D of various pain relievers in different representations, using the default Blinn-Phong shader and a vdW surface around acetaminophen.

Visualize your chemicals in 3D

ChemDoodle 3D focuses on allowing you to produce high quality graphics for small molecules. This include labels, different representations, bonds that rotate towards the camera, atom and bond highlights and more. Use ChemDoodle 3D to visualize your drawn structures from ChemDoodle desktop.

Intuitive Controls

ChemDoodle 3D’s building controls are made to clearly model the atoms and bonds they manage. Copious visual feedback is provided. There are also many options for customizing the building tools to your preference.

6 Bond Types

6 physically relevant bond types are provided to create any type of chemical representation. No other program compares.

Smart Bonds

ChemDoodle 3D renders multiple bonds that are able to orient themselves towards the camera for the most descriptive graphics.

Optimize Zone

When building 3D structures, ChemDoodle 3D will automatically suggest the best place in three dimensions to add an atom connection. This helps you quickly build molecules. You can then simply turn on the minimizer to optimize physical coordinates. No other program has an optimize zone like ChemDoodle 3D’s!

Balls and Sticks

You have full control over how atoms and bonds are rendered, and you can quickly choose from predefined representations, such as van der Waals spheres, ball and stick, stick, wireframe and line.

Show Labels

ChemDoodle 3D’s advanced graphics engine can render text beautifully. Use this to show atom labels. You have full control over font, size and color.

Add Hydrogens

Hydrogens will be added for you to your structures in appropriate 3D locations.

Implicit Hydrogens

Implicit hydrogens are automatically tracked for your structures, but you can also override them as appropriate.

Aromatic Representations

Use toruses for aromatic circles or use resonance bonds that automatically orient to the center of rings.

Optimize Structures

Quickly generate 3D coordinates for your structures using several algorithms.


Measure distances, angles and torsions in your structures.

Cheminformatics Functions

Quickly access powerful functions to help modify your graphics: saturation, Kekulization, ring perception, distance geometry embedding, and more.