We are pleased to introduce version 6.5 of our ChemDoodle 3D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $15, and we have a free trial available at: https://www.chemdoodle.com/3d

Let's print some 3D models

ChemDoodle 3D has the ability to output model files from the molecules and objects you create. We print some of these model files using a 3D printer.

Executive Summary

ChemDoodle 3D v6.5 is a feature update to ChemDoodle 3D. You can now export your created molecules and chemistry scenes into model files for 3D printing and other CAD applications. Many formats are supported, along with thorough mesh data output and options for each type. We have also added support for three more RCSB formats: BinaryCIF, PDBx/mmCIF and PDBML. The last major new feature is CIP stereochemistry support for cumulenes.


  1. Export your ChemDoodle 3D creations into many popular 3D model file types for import into other CAD applications and for 3D printing:
    1. 3D Manufacturing Format {.3mf}
    2. Additive Manufacturing File Format {.amf}
    3. COLLADA Digital Asset Exchange {.dae}
    4. Extensible 3D Graphics {.x3d}
    5. Polygon File Format {.ply}
    6. STereoLithography {.stl}
    7. Virtual Reality Modeling Language {.wrl}
    8. Wavefront Object File {.obj}
    ChemDoodle 3D supports as much of each format as possible, including meshes, normals, materials, transparency, colors and multicolors. Note some formats are less capable. For instance, the STL format cannot store colors, so use a more capable format like the VRML formats to suit your application. ChemDoodle 3D implements many format specific options, such as both binary and ASCII support for STL and PLY files and caching and compression for VRML files.
  2. Added support for cumulene CIP stereochemistry, M and P. You may also display these as Ra and Sa (axial chirality).
  3. Added support for three new RCSB formats: RCSB BinaryCIF (.bcif), RCSB Macromolecular Crystallographic Information File (.cif, .mcif, .mmcif) and RCSB Protein Data Bank Markup Language (.xml, .pdbml). Both input/output of small molecule information and full model input are supported.
  4. You may now manually edit atom charge values (including non-integer values) using the Molecule>Edit Atom Charges menu.
  5. Changed the default nucleic acid ladder platform color to blue.


  1. Fixed issue where the applied scene texture is not removed upon restoring style sheet defaults.
  2. Changing stereochemistry view from E/Z to cis/trans and vice versa now takes effect immediately.