powerful interface
ChemDoodle 3D allows you to visualize and interact with chemical and biological information in 3D. It is very powerful, yet still easy to use. The above image shows many of the controls available in ChemDoodle 3D for creating your 3D scenes with advanced graphics algorithms and effects.

Powerful and intuitive tools

ChemDoodle 3D is an advanced system for creating 3D scientific graphics. The entire foundation is built from the ground up to provide the best features, from the complete customization, to the advanced picking system, to the multi platform graphics support, to the text and shader systems. ChemDoodle 3D was designed to work as you envision it and produce the graphics that you imagine.

Completely Customizable Graphics

All the rendering in ChemDoodle 3D is controlled by visual specifications that are defined by you. The specifications can apply to the entire scene, selected content or individual objects.

Advanced Selection System

ChemDoodle 3D provides tools for picking content directly from the scene. There is also a very thorough selector window for precisely selecting content that will show you what you are hovering. You can also select content via keyboard shortcuts and by SMARTS.

Advanced Text System

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


Control the color and direction of the lighting.


Fully customizable real-time dynamic shadows add a major sense of realism to your graphics.


Define fogging using linear, exp1 and exp2 algorithms. Give incredible depth to your graphics or focus on specific parts with these features.


Include a compass on the bottom left of the graphic, or in the center overlaying the content to describe orientation.


Shaders are advanced instructions on how 3D graphics are generated. ChemDoodle 3D provides you with several built in shaders to render your graphics, from realistic styles like plastic, to unrealistic styles like cartoon.

After Effects

After effects are multipass shader options that provide additional graphical effects. Blurring and outlining are currently available.


Both orthographic and perspective projections are available and can be switched instantly.

Mesh Quality

You can quickly switch between various quality levels to benefit graphics quality or to speed up performance.


ChemDoodle 3D provides inertia and animations. Inertia will set your molecule spinning in the direction you flicked it, while animations provide continuous movement. Rotations, rocking and yo-yo animations are available. You can fully control these animations as well as the framerate.