There is a new feature update to ChemDoodle 3D today. Please see below for changes. These new updates require our new subscription (or lifeltime) licenses, which can be purchased in our store. Site licenses get free access to the latest updates. To download the latest versions, please visit our download page. As always, if you have any questions, suggestions or bug reports concerning iChemLabs software, please contact us.

Executive Summary

This is a feature update to ChemDoodle 3D v5. Major changes include new 3D stereochemistry support and better feedback when force field atom mapping issues occur.


  1. 3D structures can now be handled by our advanced CIP stereochemistry engine. Chiral centers will be assigned R and S configurations, while both cis/trans and E/Z configurations can be deduced on double bonds. Configurations will update in real time as you edit molecules in 3D space. This is the exact same accurate CIP engine from ChemDoodle 2D, so you can be confident in the results.
  2. Force fields now report both warnings and errors when resolving the structure. Warnings will still allow optimizations, but calculations will be dubious.
  3. Minimizer widget will now show specific warnings and error descriptions for molecules that fail to resolve.
  4. UFF will now show incompatible structure errors for 0 order bonds (bond contributions use ln(0) = -infinity).


  1. Fixed bug where double clicking on a file to open on Windows did not work properly.
  2. Corrected some issues with the copy/paste and read/write of measurements.
  3. Included missing executable details for Windows.
  4. Included more application registry keys on installation for Windows, including DisplayVersion, which is required for many management systems.