ChemDoodle 3D | Molecular Modeling and Graphics Software

for Windows, macOS and Linux
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Looking to create 2D drawings for molecules and chemistry?Check out ChemDoodle 2D →↓
2D Chemical Drawing, Publishing and Informatics
ChemDoodle 3D is a powerhouse for working with chemistry in 3D with industry leading molecular modeling tools and best-in-class graphics.
We spend a very long time scrutinizing the models generated in ChemDoodle 3D. Take a close look at the renderings as you are rotating them to watch bonds orient towards the camera; every object mesh in the scene is built to merge with the others; and our models are some of the most gorgeously crafted by any software in this industry.
All of the rendering in ChemDoodle 3D is controlled by styles defined by you. The styles can apply to the entire scene, selected content or individual objects.
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.
In addition to the predefined Jmol, Rasmol, PyMOL and CDK color sets, you can also manually define your own elemntal color set to apply to molecule rendering.
Include a compass on the bottom left of the graphic, or in the center overlaying the content, to describe orientation.
Both orthographic and perspective projections are available and can be switched instantly.
You can quickly change between various quality levels to benefit graphics output or to speed up performance.
Transparency effects are just that, they let you see through objects in the scene. ChemDoodle 3D allows you to render transparent objects with or without back faces.
ChemDoodle 3D can generate a number of surface types and color functions for any number of atoms. Visualize the space of your structures in ways other editors cannot.
You can customize mesh algorithms, display types, normals, colors and more.
Different types of surfaces are available, including van der Waals (VDW), solvent accessible surfaces (SAS) and solvent excluded surfaces (SES, Connolly).
Color your surfaces through various functions to provide a physical perspective on the structure. Functions include by atom color, charges (Gasteiger, QEq, QTPIE), lipophilicity (AlogP98) and molar refractivity (AMR98).
View atomic orbital models based on quantum numbers with the Orbitals widget. Many options are available for customizing the graphics, which can then be output to an image. A great way to view the different orbital shapes.
Gamma correction alters the brightness model of the graphics to compensate for the non-linear brightness physics of your monitor. ChemDoodle 3D defaults to a standard value of 2.2, but you can change this as appropriate for your screen.
Shader programs are advanced instructions sent to the graphics card on how 3D graphics are generated. ChemDoodle 3D provides you with several built-in shaders to render your graphics, to create realistic styles like plastic and unrealistic styles like cartoons. Shaders in ChemDoodle 3D also provide additional features, such as outlining and shadows.
Control the color and direction of the lighting.
A shading model is the method for converting the scene information into colors implemented by the shader program. Ambient-Diffuse-Specular (ADS) theory can be implemented in many different ways to create shaders that produce realistic graphics and non-realistic graphics. ChemDoodle 3D implements the following shading model types to choose from, all based on the ADS shading model:
A renderer is the complete procedure in which we communicate with the graphics card using one or more shaders to produce a final image. In the simplest procedure, a single call is made to the graphics card where we pass in the scene data and produce an image with a single shader program. This is what we call a forward renderer.
The downside of a forward renderer, is each pixel is calculated in isolation, limiting the techniques we can achieve. We can instead chain several rendering passes through the graphics card together, using the output of one complete pass as input into another. This allows the software to produce some advanced effects.
In ChemDoodle 3D, you will find styles for 3 different types of renderers: (1) the forward renderer (2) the deferred renderer and (3) after effects.
Anti-aliasing smooths out the rough pixel edges in graphics (known as jaggies). ChemDoodle 3D supports hardware Multisample anti-aliasing (MSAA) for the forward renderer and both Fast Approximate anti-aliasing (FXAA) and Subpixel Morphological anti-aliasing (SMAA) for the deferred renderer.
Fully customizable, real-time, dynamic shadows add a major sense of realism to your graphics.
Textures apply a surface styling to the objects rendered in the scene. This is done by defining some pattern in three dimensions, similar to how you would see three dimensional patterns if you were to cut into a block of wood. The objects are then crafted out of this pattern to produce the graphics, allowing you to produce a number of interesting styles. Choose from granite textures, wood, stripes and more.
Define fogging using linear, exp1 and exp2 algorithms. Give incredible depth to your graphics or focus on specific sections with these features.
Screen space ambient occlusion (SSAO) simulates the occlusion of ambient light in corners and crevasses of 3D objects. If you look in the corner of your room, it will appear slighly darker than the centers of the walls. This technique adds a significant amount of realism to the image and greatly helps with perception of topography. This technique is fully customizable in ChemDoodle 3D.
Outline effects are created by finding significant changes in cached data values from pixel to pixel. There are two types of outline algorithms provided in ChemDoodle 3D: Trace and Artistic. You can control colors, thicknesses, sketchiness and more!
A depth of field effect focuses in on a specific portion of your scene, emulating images made with camer