In addition to creating beautiful graphics for small molecule structures, ChemDoodle 3D will also help you to edit and create graphics for protein and nucleic acid macromolecules. The above image was rendered in ChemDoodle 3D of Protein Data Bank entry 5LRS with two solvent accessible surfaces rendered for the protein chains and using the None shader.

3D scientific graphics, big and small!

Visualization of macromolecules like proteins and nucleic acids are essential for the communication of scientific information. ChemDoodle 3D offers a wide range of control for creating publication quality graphics.

Protein Data Bank Format

ChemDoodle reads protein and nucleic acid information from PDB files and generates high quality meshes that are superimposed over the atom and bond coordinates.

Macromolecular Transmission Format

ChemDoodle also fully supports the RCSB Macromolecular Transmission Format for incredibly fast input of Protein Data Bank files with full bond order information.

Protein Ribbon Models

Beautiful protein ribbons and traces are generated. Tubes, cylinder and plank models and cartoon models can also be generated. These models can be segmented, colored and completely controlled through visual specifications. For instance, you can change the ribbon thickness or the alpha helix width.

Nucleic Acid Ladder Models

Accurate nucleic acid ladder models are generated. These models can be colored and completely controlled through visual specifications. For instance, you can change the backbone thickness or the platform height.

Interpolation Algorithms

ChemDoodle 3D can use either a B-Spline algorithm or the Catmull-Rom algorithm for generating models. The Catmull-Rom spline creates more accurate models, but the B-Spline algorithm produces smoother and more aesthetic results.

Residue Atoms and Bonds

Control residue atoms separately from the rest of the data for unique graphics.


Show and hide water atoms defined in PDB files and represent them with stars instead of spheres.