ChemDoodle 4.1.0 has been released! We provide this upgrade, free of charge, to our existing customers.

Executive Summary

This significant update brings dozens of new features and fixes recommended by our users. Included are a significantly improved rendering engine, autosaving, 52 new glassware templates (and the ability to flip them), high-quality bitmap image output control, and other new features. Significant fixes include the disabling of terminal carbon label display by default, the restoration of PubChem functionality in the MolGrabber widget, greatly improved ChemDraw file reading, fixing of all known stereochemistry detection issues, and much more.


  1. The rendering engine has been upgraded with additional improvements. Bond joins will now look nice regardless of the end cap chosen. The default end cap is now butt for flat bond ends and sharp looking structures. The second line in double bonds will now be placed more appropriately when in constrained structures, such as norbornadiene. Symmetrical double bonds will now extend to connect to the bonds they attach to. Protruding bond merging to multiple single bonds has been improved. Protruding and bold and thin double bonds now merge. Atom labels will now base their vertical alignment on a non superscript or subscript token if a superscript or subscript token is the attachment point. A visual specification to control bond merging is now provided.
  2. Autosaving. Your work is now automatically saved. The defaults can be configured in the Preferences window under the Saving tab. You can turn autosaving on and off, and change the save interval. By default, the save interval is 5 minutes.
  3. 52 new glassware templates.
  4. Glassware templates can now be flipped.
  5. Bitmap image output is improved. The image scale is now definable for each output image. The default scale is 4x. JPEG and PNG output can now define DPI for high quality printing when scalable vector graphics are not an option. The default DPI output is 300dpi. Transparency can now be defined in formats that support it. The defaults can be configured in the Preferences window under the Advanced tab.
  6. A new menu item to optimize a PDB file to ChemDoodle Web Components JSON for fast loading and manipulation.
  7. A new pinwheel color chooser is provided on all platforms. The color chooser is much improved on Windows/Linux, with new panels for more robust color picking.
  8. Arrowheads now shrink when their length is greater than half of the line length.
  9. JCAMP spectra are now written.
  10. Added a new option to control if Hz are automatically converted to PPM from input JCAMP spectra. This is enabled by default.
  11. Line notation formats will now recognize multi-line input.
  12. The widget dock is now movable.
  13. Added a new specification to control the width of the outlines for atoms represented by circle graphics.
  14. EPS and SVG output now includes ChemDoodle metadata for round-trip editing.
  15. The site license configuration now contains master controls to disable/enable updates and expiration notices.


  1. PubChem searching in the MolGrabber widget has been restored.
  2. The automatic display of terminal carbon labels is now disabled by default. You can turn them back on in the Preferences window, under the Visuals tab under the Atoms sub-tab in the Carbons section.
  3. ChemDraw files are now read in with finer attention to detail. Text boxes appear correctly and alignments are now read, arrow heads more closely match their size, curved arrow coordinates have been corrected, attribute locations are better calculated, charges and radicals are no longer duplicated graphically, bold and formatted labels are now read, charges will be surrounded with circles if detected, show/hide of carbon labels is now adhered to, wavy bond specifications are set, terminal carbon label and implicit hydrogen settings are read.
  4. Fixed a couple NMR simulation issues. Alcohols are now recognized when connected to aromatic rings. Alcohol shifts next to aromatics are improved.
  5. Fixed bug where stereochemistry in very complex structures with many condensed labels were not being determined correctly.
  6. Stereochemistry will no longer be defined to aromatic bonds like in benzene.
  7. Fixed issue where forcing E/Z stereochemistry did not update atom label positions.
  8. Improved the performance for detecting stereochemistry in complex structures with many condensed labels.
  9. Fixed bug where forcing cis/trans stereochemistry to a non-applicable double bond would cause an error.
  10. Stereochemistry is now detected for double bonds in structures with condensed labels.
  11. Glassware templates now correctly show default stroke colors.
  12. Fixed issue where some glassware templates were not being correctly drawn.
  13. CML output now correctly defines namespaces.
  14. X-axis offsets are now read in from JCAMP files.
  15. SLN input is now read correctly, even if there are atom id clashes.
  16. Fixed issue where the SMARTS matcher was not correctly matching some aromatic bonds.
  17. Improved the maximum activation message to explain how to deactivate/reactivate ChemDoodle.
  18. Fixed bug where XLogP v2.0 calculations were not consistent and were inaccurate.
  19. Bonds no longer withdraw from atoms represented by circle graphics.
  20. The buffer between a reaction arrow and its constituent structures has been reduced by half when cleaning.
  21. ChemExper supplier searches now include explicit hydrogens.
  22. Fixed bug where drawing a double lined arrow would set the default line style to be doubled.
  23. The color button is now clearer when empty colors are defined.
  24. Fixed bug where the template widget would have some issues if it was defined as the default widget.
  25. The Line Notation Pad widget now lays out multiple discrete molecules.
  26. Fixed issue where colors in text areas were not being saved.
  27. Fixed issue where opening a text field/area and then changing tabs caused the text component to remain open.
  28. Fixed issue where sometimes the default document style sheet was being incorrectly overridden by the current style sheet.
  29. Fixed EPS bug where some output would disappear when rotated text areas were present.
  30. Fixed bug where the radical attribute button would place a charge instead.
  31. Fixed issue where MDL CT file output had labels right-aligned, while still valid, some other applications require them to be left-aligned.
  32. Fixed a couple interface issues, such as how drop down menus would close when the mouse scroll was used.
  33. Fixed bug where interface settings were not being stored with the workspace.