surface calculation
A solvent excluded surface generated for Sildenafil. The surface is rendered as an opaque solid with shininess using the default Blinn-Phong shader. The surface is colored using a QTPIE function and a Coulomb potential.

Go beyond just balls and sticks

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.


Generate surfaces for groups of atoms. Customize mesh algorithms, display types, normals, colors and more.

Surface Types

Different types of surfaces are available, including van der Waals (VDW), solvent accessible surfaces (SAS) and solvent excluded surfaces (SES, Connolly).

Color Functions

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).