Macs in Chemistry

Insanely Great Science


ChemDoodle 2D v12 is Unveiled

iChemLabs have just announced the release of the hugely popular ChemDoodle 2D v12.


ChemDoodle 2D v12 presents a new, refreshed interface. We took a close look at every component, icon, window and form inside of the application to optimize and beautify our users' experience. The main interface has been reorganized. Many usability issues have been resolved. Most users will find the changes to be straightforward and the underlying chemistry functionality of the software is unchanged. We have a very quick guide to help you with the bigger changes below. In addition to the interface, improvements have been made to our chemical image recovery (CIR or OSR) function, IUPAC naming, the atom and bond joining function, and our user guide.


ChemDoodle 2D v11.13 Update

ChemDoodle 2D v11.13.0 is a feature update wrapping up their latest massive work on stereochemistry. A new advanced CIP descriptor engine is implemented for the most accurate and consistent CIP assignments and the MDL/BIOVIA stereochemical drawing interpretation algorithm is now implemented along side the IUPAC specification. iChemLabs believe ChemDoodle is now the industry leader for handling stereochemistry, especially in 2D drawings. Several improvements are also included.

This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $18, and they have a free trial available at:


ChemDoodle 2D and ChemDoodle 3D on Apple Silicon

A latest news from iChemLabs highlights Apple silicon support for ChemDoodle 2D and ChemDoodle 3D As the plot below shows there is a significant boost in performance.



ChemDoodle 2D v11.11 Update Available

The very popular chemical drawing package ChemDoodle has been updated

ChemDoodle 2D v11.11 is another feature update focusing on our main topic this year, stereochemistry. Stereochemical projections will now be automatically recognized and stereochemical features will be analyzed. Fischer, Haworth and chair projections are supported.

This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $15, and these is a free trial available at:


ChemDoodle 2D update

An updated version of this very popular chemical drawing package is available. ChemDoodle 2D v11.10 is a free update.

ChemDoodle 2D v11.10 includes further advancements to our cheminformatics functions along with some new features. The stereochemistry engine has seen a complete rewrite, with a brand new system for evaluating stereogeometries in OD/2D/3D, leading to accurate generation and interpretation of wedge drawings and full support for stereochemistry in SMILES protocol. Further advancements in our industry-leading 2D coordinate layout algorithm are provided. New features include ring coloring for highlights, support for group objects in ChemDraw files, checking bonds for drawing warnings, new periodic table options and more. For macOS users, the QuickLook plugin is now functional on the latest macOS versions.


ChemDoodle 2D updated


The very popular chemical drawing application ChemDoodle has been updated to version 11.8

ChemDoodle 2D v11.8 includes significant improvements to many features, including excellent chain replacement nomenclature in IUPAC naming, support for allene/cumulene stereochemistry, improved bezier curve tools, current InChI support and more file options.

Full details of the update are here

You can get all the ChemDoodle applications (ChemDoodle 2D, 3D and mobile) for a single monthly ($15) or yearly subscriptions ($100), and as a one off lifetime purchase ($750).

More details on the store


ChemDoodle 2D update


The very popular chemical drawing package ChemDoodle 2D has been updated to version 11.6 Release details.

Handling relative and absolute stereochemistry of molecules is a major challenge and this release of ChemDoodle provides an enhancement to the the ability to define, edit, input and output enhanced stereochemistry definitions to a handful of compatible file formats.

Enhanced Stereochemistry. You may now define enhanced stereochemistry for chemical structures, using or and & modifiers. All stereocenters are absolute (abs) by default. Groupings will be automatically determined via incrementation, but you may also manually define group numbers for more advanced stereochemistry queries. Enhanced stereochemistry definitions are read and written from ChemDoodle Documents, ChemDoodle JSON, ChemDraw files, ChemAxon Marvin Documents and MDL CT files (limited in v2000, full support in v3000).



ChemDoodle 2D v11.5 has been released


ChemDoodle 2D v11.5 is a feature update. This update is all about databases. Google Patents is integrated to allow you to search the Google Patents and non-patent literature databases using structures drawn in ChemDoodle. The SciFinder-n interface has been improved and updated. A new PubChem protocol, PUG, replaces the old Entrez protocol for better results from the MolGrabber widget. RCSB PDB database connections have been switched to HTTPS. Additions

  • Google Patents searching is integrated. You may perform structure, substructure and similarity searching into the Google Patents and non-patent literature databases at Google using structures drawn in ChemDoodle.
  • The SciFinder-n interface has been updated and improved for better usability and with a UI matching the current SciFinder-n product.
  • PubChem access now uses the PUG REST protocol, which results in more stable communication with the PubChem database and higher quality results when using the MolGrabber widget.
  • Updated import of MMTF/PDB data from the RCSB.
  • There is now an option to disable the native file choosers used by ChemDoodle in the Preferences window, under the Files tab. Disable the native file choosers if you are having issues with them, for instance if you have a problem with iCloud on macOS and cannot get the file choosers to load.

More details here.


ChemDoodle 2D v11.4 Update Available


A new version of ChemDoodle is available, this is a free update for all subscribers.

Whilst there are a few bug fixes and stability improvements the big news is the new feature enabling generation of a chemical structure from an image.

ChemDoodle now has the ability to recreate a chemical drawing from an image of a molecule, recovering the original chemical data. This function is performed using the File>Recover from Image... menu item. This function is different from inserting the image as inserting an image provides you with just a graphic, while recovering the chemical drawing allows you to regain access to the chemical information to use or edit further. We call this function Chemical Image Recovery (CIR). Some may also refer to this function as Optical Structure Recognition (OSR).

I can see this being a very popular feature.


ChemDoodle 2D v11.3 Update


I just heard version 11.3 of ChemDoodle 2D software has been released.

ChemDoodle 2D v11.3 is a feature update. The main new feature is expert IUPAC naming support for free radicals. Other major features include new image output sizing options with previews, and stoichiometry table options.

ChemDoodle 2D is a popular and extensively featured Chemical Drawing and cheminformatics software tool.


ChemDoodle 2D v11.2 released


A really interesting update to the popular chemical drawing package ChemDoodle.

The focus of this update is chemical data recovery. You can now copy and paste chemical figures (regardless of the chemical software use to create the figures) from applications on Windows and macOS into ChemDoodle to recover the original chemical drawings for extraction and further editing. We also have a new tool in ChemDoodle for searching Microsoft® Office files to extract chemical drawings if you do not have access to the original operating system or Microsoft Office anymore. This update includes significant work on CDX and CDXML file support with a goal of reproducing graphics in a pixel-perfect manner.

One of the major benefits of this is it allows macOS users to finally collaborate with Windows users in creating chemistry documents. You can use the MS Office recovery tools in ChemDoodle to extract and edit figures created on different operating systems!



ChemDoodle Mobile (progressive web app) Updated


Just noticed this.

ChemDoodle Mobile Updated.

There is a big update to ChemDoodle Mobile today! The interface has been completely redone, and is much more user friendly. There are now a total of 11 tools, including IUPAC naming, CIP stereochemistry analysis, reaction balancing, exploring databases like the RCSB PDB and IZA, and drawing and saving chemical figures. Feel free to request additional tools. Access to ChemDoodle Mobile is included with all active ChemDoodle licenses.


ChemDoodle 2D updated


The very popular chemical drawing package ChemDoodle has been updated.

ChemDoodle 2D v11.1 is a feature and stability update and is recommended for all users. The major new feature is advanced repeat unit support, both in graphical drawing and cheminformatics interpretation and expansion. Other notable features include improved reaction building interfaces and feedback, arc-length controls, and smaller EPS file output. This update also corrects an issue introduced by macOS 10.15.6, leading to corrupted and missing windows. So if you are experiencing these issues, make sure to install this update.


ChemDoodle 2D v11 is Released


The latest update to the very popular chemical drawing package ChemDoodle has been released. This update brings fully chemically aware and self-calculating stoichiometry tables, automatic electron pushing arrows, and with the ability to recover chemical data embedded in Microsoft Office files.

Chemical data recovery from Microsoft Office files: (experimental feature) Round-trip editing is the process of embedding data from one application into another, that can then be recovered later. Chemists use this all the time when creating chemistry documents in Microsoft Word. ChemDoodle 2D has provided round-trip editing functionality on Windows, macOS and Linux since its inception and starting with version 10.4, users can paste chemical data from embedded ChemDraw images on macOS in ChemDoodle 2D.

However, there are several issues when relying on round-trip editing, as the user may not have continued access to the originating chemistry program or Microsoft Office, or may be working with an individual on a different operating system. Several times, Microsoft has removed the round-trip editing functionality in Office products. In all of these cases, the chemistry data in these files cannot be used. ChemDoodle 2D now provides a very unique solution for this problem, and can search and extract chemical data embedded in Microsoft Office files, regardless of the program they were created in, including ChemDoodle, ChemDraw, ChemSketch and Biovia Draw, and regardless of the operating system. You can now recover your chemical data from Word documents you created on Windows if you switch to Linux, and you can now edit chemical figures from a Word document on macOS with ChemDoodle from a colleague who uses ChemDraw on Windows.


ChemDoodle 2D v10.4 Update Available


I just heard about a new update to ChemDoodle today, and this looks like a really significant update.

This update includes a number of features, and improves several aspects of the application. We continue to improve our 2D structure cleaning algorithm, this time with a focus on structures with unavoidable overlaps when standard angles and lengths are used. ChemDoodle can now accept pastes of ChemDraw® PDF on macOS, recovering the original ChemDraw data; this essentially allows you to recover chemical data from ChemDraw images pasted into programs like Microsoft Office on macOS. A number of other smaller features is included based on customer feedback. This update is recommended for all users.

This will be a really popular addition, greatly helping interoperability.

The full release notes are here


ChemDoodle Web Components v9 is Available


Version 9 is a major update to the ChemDoodle Web Components library. There has been a complete refactor of the library to ES6 best standards. The sketcher and editor UIs have been improved with SVG button icons. New Cloud features include advanced CIP stereochemistry support, reaction equation balancing, and stereochemistry enforcement in mechanism matching. The ChemDoodle Web Components website has been recreated to be responsive, much easier to read, and support high-DPI displays for clarity.

The website has some great examples of what can be generated.



ChemDoodle v10.2 Released


The latest update of the popular chemical ChemDoodle 2D drawing package has been released.

This is a significant feature update to ChemDoodle 2D v10. This update is recommended for all ChemDoodle 2D users. Major changes include an updated shape system allowing you to edit shapes while you draw them, greatly speeding up figure drawing. A significant amount of work has culminated in a brand new and powerful table tool for creating rich data graphics. ChemDoodle 2D can also now balance any drawn reactions or typed chemical equations.


Full release notes are available here

In particular note

Quicklook plugin works again and has been rebuilt with the latest version of Xcode on Catalina.


ChemDoodle tools to search in SciFinder


Starting with ChemDoodle 10, new tools are included for directly querying substances, reactions, references and suppliers in SciFinder

“We are proud to extend our collaboration with CAS to introduce a direct integration of our desktop ChemDoodle software with SciFindern” said Kevin Theisen, President, iChemLabs, LLC. “Our focus is to provide the best experience for chemistry researchers. By streamlining the communication between ChemDoodle and SciFindern, this integration increases researchers’ efficiency and optimizes the workflow between these popular applications.”


iChemLabs and SciFinder-n


Just got this update from iChemLabs the developers of ChemDoodle.

"iChemLabs customized one of the leading chemistry sketchers and graphics drawing tools for the new SciFindern interface,” said Kevin Theisen, President, iChemLabs, LLC. “Our collaboration with CAS has been very successful in helping researchers develop and visualize better chemical structures more rapidly within SciFindern, and we look forward to continuing to provide SciFindern users with this best-in-class experience.”


ChemDoodle 9.0 released


I just saw that ChemDoodle 9.0 has been released and I plan to have a detailed look later this month.

ChemDoodle 9 is a major revision of every aspect of the software. We spent over 2 years overhauling and improving the cheminformatics engine, interface, drawing controls, image and chemical file types, graphics, and operating system compatibility. In addition to the new features, the entire codebase has been refactored for the current best standards to take advantage of the latest performance, memory and security features of the operating system.

What is new in ChemDoodle 9

  • A new user manual discusses all the new features in detail over several pages, too many to list here. (click to load manual, section 1.2)
  • Drawing and Graphics – Tons of new systems for making your graphics quicker. Auto-placement of attributes (charges/radicals/stereocenters/etc.). An improved text tool that can create both atom text and formatted captions. Draw chiral carbon nanotubes in addition to zigzag and armchair. New dynamic brackets and structure highlights. Better drawing tools for advanced figures.
  • Chemistry – State-of-the-art implementation of the most recent CIP rules. A clearer and more powerful warning system. Advanced implicit hydrogen handling including the analysis of advanced aromatic resonance systems. Full support for the latest elements as defined by IUPAC and much more!
  • Interface – A brand new customizable cursor system, improved IUPAC name-to-structure interface. Improved color palettes, now with Rasmol, CPK and Custom color sets. HTTPS support for PubChem is now implemented for access in MolGrabber. Improved color choosers including alpha support and high resolution improvements across the entire application.
  • Chemical Files – The Nature style sheet has been added. SMILES interpretation has seen significant work, with a focus on very advanced cheminformatics techniques. Added support for the RCSB MacroMolecular Transmission Format (MMTF). More support for ChemDraw, MDL CT, MRV and ISIS/Sketch files.
  • Images – TIFF images can now be exported with custom DPI settings. GIF image output can now have semi-transparent pixels merged with white. Added viewBox attribute for SVG. When saving files, you can now use alternate extensions and other image file chooser improvements. Control which image file types are shown in the save image choosers.
  • Vector Art – New glassware graphics have been added as well as dozens of new BioArt.
  • Customizability – The keyboard and tools shortcuts are now fully customizable by the user. The user settings folder location can now be controlled. * Custom attribute names and values are now persisted through restarts. Windows – Full support for high-DPI screens, without the manual scaling required in the past. The OLE plugin has been rebuilt for the most current compliance with Windows libraries.
  • macOS – Improved and full Retina support. Native file choosers.




I just came across a new Electronic LabNotebook (ELN), eLabFTW is an open source solution powered by PHP/MySQL in Docker containers. One install can be for a team, or the whole institution. You can also install it on your computer for a personal notebook.

All the user needs is a web browser to access the notebook.

Upload any type of files, embed images in the text, Draw doodles directly with your mouse, Use templates for your experiments, Draw molecules with Chemdoodle, REST API for accessing programmatically your experiments, SAML2 authentication if you have an identity provider, Growing community of users and contributors scrutinizing the code and improving it, Highly customizable: you can change the colors, the status list, the items types list, etc. Can fit any kind of lab (chemistry, biology, physics, astronomy, etc.)

Full details are available here and there is a presentation here

There is also a demo account available


htmlwidgets for chemdoodle web components


Just came across this site

This repo is for the creation of an HTMLWidget for visualizing moleules based on the ChemDoodle WebComponent library, the HTMLWidgets package, and the Chemistry Development Kit via rCDK.

Looks to be under active development.


Flot plots updated


I have updated the page showing the interactive plots using Flot and ChemDoodle Web Components

I have a regular need to share results from my work and historically this has been via a paper reports that have more recently been replaced by electronic versions. Whilst useful, these reports lack the interactivity, in particular it is extremely useful to be able to easily link data points on a scatter plot with the corresponding chemical structure. So I’ve started using web-based reports to add extra functionality. Unfortunately it has often required the addition of applets or plugins that I can’t be sure the viewer will have available so with the advent of HTML5 I’ve been exploring writing the reports using just HTML and javascript. One of the major challenges is to produce interactive plots instead of using static images, and I’ve been exploring the use of Flot to produce a plot with chemical structures produced using either a web-service like ChemSpider or a javascript library of web components developed by ChemDoodle.



ChemDoodle Web Components updated


ChemDoodle 8.1 available


A new update for the very popular chemical drawing application ChemDoodle has been released. Version 8.1 looks to be a significant update with several useful new features and a few bug fixes.


  • New bitmap colorspace output options: Color, Greyscale, Monochrome. The images are not just in the colorspace, but the image data is correctly defined, so that monochrome images are much smaller than grayscale, which will be smaller than color.
  • Added Functions setting to use either the Bondi or current literature value for the van der Waals radius in the VABC calculator.
  • Added support for implicit hydrogen overrides to all capable formats.
  • Added some more recent elemental data.
  • Updated and expanded vdW values.
  • Added the latest new element names from IUPAC, completing the last row.
  • Alpha colors are now stored in ChemDoodle Documents.
  • Chain tool now merges with previous drawn structures in the same manner as rings and templates. Red rings will be shown for auto-connect overlaps and this behvior can be controlled in General Preferences. All issues involving drawing chains on top of previous structures have been resolved.
  • Auto-connect range when drawing rings, chains and templates is now controllable in General Preferences.
  • Added option to suppress implicit hydrogens from groups 1-12.
  • Functional hydrogen settings have been moved from Atom Visuals Preferences to Functions Preferences.
  • Added more refined options for controlling double bond symmetry. Now terminal double bonds connected to a ring can be made symetrical as a case.
  • Updated to OPSIN 2.1.
  • OPSIN warnings now still produce a result and display an appropriate warning instead of failing.
  • Added templates for tetroses.
  • Keyboard shortcuts have been added for the atom label tool, so you can bold, italicize and underline text via the keyboard.


  • Added HTTPS support for NIH Cactus, returning functionality to the 3D clean tool.
  • Corrected Elemental Analysis and Mass Parent Peak simulation results for structures with multiple charges.
  • Addressed a number of issues for implicit hydrogen calculations in resonance systems.
  • Fixed issue where arbitrary rings and and crown ethers drawn to a bond of length that was different from the standard length didn’t work properly.
  • Fixed bug where Preferences boolean button sets were flagging visuals changes for non-visual settings.
  • Fixed incorrect behavior where General or Advanced Preferences settings were falsely notifying the user of style sheet changes.
  • Fixed issue where output ChemDoodle 3D Scene (ic3) files from ChemDoodle were flipped on the y-axis.
  • Corrected a number of minor graphical glitches with vertical connections and wedge/bold bonds.
  • Closing the color select window no longer conforms colors, but does update the color button.
  • Using the color scrubber of the Quick Colors button now also sets the selection to that color after choosing.
  • Quick Colors button now correctly adjusts an entire label, even if chemical interpretation is off.
  • Minor updates to the Periodic Table.
  • The Center>Selection menu items are now correctly context sensitive.
  • iChemLabs extensions to JCAMP DX files have been removed and are no longer necessary. Note that older JCAMP spectra written from ChemDoodle that used these extensions (typically simulation output) will not be able to be read anymore.
  • Fixed rare crash that occured when Preferences bounds somehow ended up out of the defined bounds.
  • Fixed some minor IUPAC naming issues.
  • Isotopes from ChemDraw files are now displayed correctly.
  • Isotope labels are now correctly accounted for in bond retraction.
  • Ring, chain and template actions that don’t actually change the document are now ignored in history.
  • Minor text sizing considerations and corrections.
  • Kekulizer now ignores zero order bonds.
  • Improved text layout in tabs not to overlap with close buttons.
  • Restoring the document now correctly updates the History widget.
  • Restoring the document now correctly clears the selection if there is one defined.
  • Fixed issue where loading an autosave didn’t correctly enable the Restore menu item.
  • Fixed issue where dialogs were not reappearing after being deiconified.
  • Carbon labels will now be displayed in the implicit hydrogen count is overridden to 0.
  • Fixed the Login window cutoff.
  • Completely uppercase element symbols are now correctly handled when reading in MDL CT files.


ChemDoodle 8.0.1 is now available.


Just noticed this message.

ChemDoodle 8.0.1 is now available. However, automatic update is not allowed for Mac OS X. You must manually update ChemDoodle by downloading the latest version of ChemDoodle from, and re-installing it. NOTE: You must close ChemDoodle before re-installing the new version.
Changes in ChemDoodle 8.0.1
Executive Summary
This is a minor update fixing issues brought to our attention since the ChemDoodle 8 launch. For changes to version 8, scroll down.

  1. Periodic table should now open again from the View menu.
  2. Fixed the interpretation of deuterium and tritium in complex condensed labels.
  3. Charges in left oriented labels are now located in better positions.
  4. Default cyclopentadiene and cycloheptatriene tools now place saturation on the sprout point unless not chemically feasible.
  5. Adding rings and templates will no longer merge multiple atoms into a single point if multiple adding atoms are within the merging distance of a present atom.
  6. Fixed rendering of Bold and Thin double bonds when in perspective merges.
  7. Improved the vitamin templates.
  8. Added feature to lock polyline drawing to the horizontal and vertical positions if the shift key is held down.
  9. Flipping while retaining stereochemistry now accounts for meso centers.
  10. Torsion bond function now preserves stereochemistry if set to do so by the option under the Functions tab in Preferences.
  11. Search widget will no longer execute a search when the drop panel is empty.
  12. Fixed issue where single atom results were not rendered in the Search widget.
  13. Search widget results are now sorted with hits appearing first.
  14. Search widget searches with stereochemistry defined in query structures now work properly.
  15. Fixed bug where the Search widget could not be manually stopped.
  16. Fixed bug where query labels would disappear in the document after being dropped in the Search widget.
  17. Fixed minor SKC import issues with text labels.

ChemDoodle 8 is a massive update to ChemDoodle. Included are hundreds of new features and improvements, recommended to us by users like you. Enjoy and please spread the word!
New Features

  1. The graphics system has been improved even beyond current industry standards for graphics. Every bond merge and pixel was scrutinized. Chemical structures have never looked better. ChemDoodle provides the best graphics in chemistry, everything else is a waste of money.
  2. Major IUPAC naming improvements, including very advanced ring systems.
  3. Full support for Retina display Macs and support for high-DPI Windows hardware.
  4. A new query structure system for defining sets of molecules and for searching partner services.
  5. New powerful tools for drawing arbitrary rings and crown ethers to atoms and bonds.
  6. Superscript and subscript merging to easily create atomic notations and other chemical text.
  7. More specific cleaning tool for adjusting only a selection of a structure.
  8. Text output options and improvements for EPS and SVG files in addition to PDF.
  9. A dramatically improved Templates widget with new and more aesthetic templates.
  10. Read in NTUPLES (multiple spectra) from JCAMP files.
  11. Added support for both the SketchEl (el) and Crystallographic Information Format (cif) filetypes.
  12. More support for working with the ChemDoodle Web Components.
  13. Dozens of new BioArt graphics.
  14. Performance improvements for faster work.
  15. Dozens more new features: two new bond types, implicit hydrogen control, automatic IUPAC locant labelling, vastly improved condensed labels, search files based on query structures, recursive SMARTS, metric support for document aids and rulers, a new precise form for scaling a specific bond, many interface improvements and so much more.


ChemBioDraw and Word 15


A reader flagged this issue for me.

Word 2016 for Mac: I can't cut-and-paste an image from a vector drawing program I am a scientist and I routinely create images in a vector drawing program called ChemBioDraw. In past versions of Word, I was always able to copy these images to the clipboard and paste directly into the text of a document. With Word 2016 for Mac, all I get is many lines of gibberish code and no image. Am I missing something, or has the ability to handle vector graphics been eliminated from the program? FYI- a friend of mine who does design is having the same problem with a CAD program.

A quick search of the ChemBioDraw support forum highlights several threads that appear to be about the same issue.

I'm a new user of ChemDraw, and I have tried to copy/paste my structure into word and just end up with heaps of text like this:

0 0 0 0 0 0 0 0 0 0 0E 3.9121 2.7155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0E 3.9385 1.8909 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 2 4 0  1 3 4 0  3 4 4 0  4 5 4 0  6 7 1 0  7 8 2 0  8 9 1 0  9 10 2 0  10 11 1 0  6 11 2 0  12 13 1 0  13 14 2 0  14 15 1 0  15 16 2 0  16 17 1 0  12 17 2 0  2 18 1 0  18 5 1 1  19 20 4 0  19

With the rather unhelpful response

Currently our products are not supported with MS Office 2016. We plan to support MS Office 2016 for the future release/update.

The only thing I can suggest in the meantime is use the "Paste as PDF" functionality, this should allow display and round-trip editing.

I did a quick test with ChemDoodle and there don't seem to be any issues with this chemical drawing programme.


ChemDoodle 3D updated


ChemDoodle 3D has been updated and in addition for a limited period any customer that upgrades to or purchases ChemDoodle 8 will receive a free license for ChemDoodle 3D v2.


New features in ChemDoodle 3D v2:

  • Full Retina display support on Mac OS X.
  • Support for high DPI Windows hardware.
  • The visual specifications of the scene can now be applied to selected content, or individual objects, as opposed to the entire scene. Right-click on objects and select the Format… menu item to show visual options for that object. New representation quick buttons are now available for modifying residue atoms and bonds, ribbon models and nucleic acid models in addition to non-residue atoms and bonds.
  • Protein and nucleic acid information can now be loaded from PDB files. Ribbon, trace and tube models can be generated for proteins. Ladder models can be generated for nucleic acids. The models are fully customizable. Control dimensions, alpha helix widths, coloring and more. Both B-spline and Catmull-Rom splines can be used to generate models. Water can be displayed as stars. Residue atoms can be controlled separately from hetatoms. Load PDB files by PDB id.
  • Periodic data can now be loaded from CIF files. Unit cells of any geometry are resolved. Functions for periodic systems will be provided in the Periodic menu. Build supercells.
  • An advanced selection system has been implemented. Select, deselect and reselect content. Select all, next molecule, inverse and by SMARTS. Use the new selection mode to select content or use the selection window to list the contents of the scene and select the content you wish to work with. The selection window is very advanced and will show you what you are currently hovering.
  • Fogging can now be defined in scenes using linear, exp1 or exp2 algorithms. Fog color can be defined as well as fog ranges.
  • A compass can be added on the bottom left of the scene or through the camera’s origin.
  • 3D scenes can now be printed.
  • Added quick quality options in the View menu to quickly switch between a range of higher and lower quality rendering settings to allow you to improve graphics or performance.
  • Image export now allows for transparent backgrounds in capable image types. This allows you to easily use ChemDoodle 3D generated graphics in various media with custom backgrounds.
  • Many new smaller features: added an option to remove shadows from text, added projection menu items, certified the correct 3D stereochemistry is generated from 2D drawings, picking can now handle any number of objects, and more.
  • Updated to support ChemDoodle Web Components v7. Shapes can now be read/written using ChemDoodle JSON.
  • Your iChemLabs account can now be accessed from ChemDoodle 3D. ChemDoodle 3D customers receive a free account for accessing ChemDoodle Mobile. If you also have ChemDoodle desktop, this is the same account.
  • Dozens more improvements and additions.

ChemDoodle 8 released


The increasingly popular chemical drawing package ChemDoodle has been updated, this is a major update to an already excellent application. There also looks to be offers at the moment so this is a great time to purchase.

What is new in ChemDoodle 8

  • The graphics system has been improved even beyond current industry standards for graphics. Every bond merge and pixel was scrutinized. Chemical structures have never looked better. ChemDoodle provides the best graphics in chemistry, everything else is a waste of money.
  • Major IUPAC naming improvements, including very advanced ring systems.
  • Full support for Retina display Macs and support for high-DPI Windows hardware.
  • A new query structure system for defining sets of molecules and for searching partner services.
  • New powerful tools for drawing arbitrary rings and crown ethers to atoms and bonds.
  • Superscript and subscript merging to easily create atomic notations and other chemical text.
  • More specific cleaning tool for adjusting only a selection of a structure.
  • Text output options and improvements for EPS and SVG files in addition to PDF.
  • A dramatically improved Templates widget with new and more aesthetic templates.
  • Read in NTUPLES (multiple spectra) from JCAMP files.
  • Added support for both the SketchEl (el) and Crystallographic Information Format (cif) filetypes.
  • More support for working with the ChemDoodle Web Components.
  • Dozens of new BioArt graphics.
  • Performance improvements for faster work.
  • Dozens more new features: two new bond types, implicit hydrogen control, automatic IUPAC locant labelling, vastly improved condensed labels, search files based on query structures, recursive SMARTS, metric support for document aids and rulers, a new precise form for scaling a specific bond, many interface improvements and so much more.

Browser plugin-free CIF visualization


A nice comparison of the options for displaying crystal structures within a browser without the need for plugins/applets.

Full blog post is here

Here we compare four open-source browser engines for plugin-free rendering of the crystalline structures in CIF format.


ChemDoodle Web Components


There is a very nice review of ChemDoodle Web Components in the latest issue of Journal of Cheminformatics 2015, 7:35 DOI

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses canvas and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.


ChemDoodle Web Components JCAMP Interpreter


Displaying spectra on the web is usually a pretty minimal experience, often simply an image file. Whilst there a number of desktop applications for viewing spectra, web-based tools were often limited to Java plugins which have now almost completely fallen out of favour.

The JCAMP data format (1) for spectra is pretty widely used and we are starting to see javascript implementations of viewers. This very nice example uses the ChemDoodle web components to display the spectra and provide interaction. Hovering close to a nucleus that has a peak correlation defined will highlight that nucleus and any other nuclei in its group along with highlighting the corresponding peak. Conversely hovering close to a peak that has correlated nuclei associated with it will highlight the set.

(1) JCAMP-DX: A Standard Form for the Exchange of Infrared Spectra in Computer Readable Form ROBERT S. McDONALD and PAUL A. WILKS, JR. Appl. Spectrosc. 42(1), pp151-162, 1988


Round trip editing


Office for Mac Preview is the open beta version of the upcoming version of Office 2016. One of the issues that crops up everytime there is an update is round-trip editing, i.e. the ability to copy and paste from a chemical drawing package into Word for example and then be able to copy and paste the structure back from Word into the chemical drawing application.

I've not tested it myself but I am assured that ChemDoodle behaves as expected.

If anyone has tested any other chemical drawing packages please let me know.




ChemDoodle Mobile has been updated.

What's New in Version 1.5.0

  • Added full 3D graphics support for 3D molecules!
  • Full support for iOS8 and the new iPhone sizes
  • Buttons are now larger on larger screens
  • Various improvements to the sketcher
  • Fixed clear button where it sometimes would not work
  • Corrected bug where stereochemistry was inverted in 3D coordinate generation
  • Resolved rare issue where the app would fail to load properly
  • Significantly increased responsiveness
  • Minor changes and fixes

ChemDoodle Mobile is the most highly rated App on the Mobile Science website and is accessed with your ChemDoodle account that is provided to you for free when you purchase ChemDoodle desktop.


ChemDoodle Web Components 7 is Available


iChemLabs have just announced an update to ChemDoodle Web Components. This is a major update to the ChemDoodle Web Components with new additions to the 3D features, most notably Pipe and Plank models for proteins and support for high DPI displays, such as the Apple Retina display.

The following pages show off some of the new features:


ChemDoodle 7 Review


ChemDoodle is now firmly established as one of the key chemical drawing packages that offers an inexpensive alternative to some of the increasingly expensive drawing packages. It also has the advantage in that it supports Mac, Linux and Windows and offers access to ChemDoodle Web Components. I’ve written a review of the latest update.


Status of WebGL

Here is an interesting article highlighting the current status of WebGL. WebGL is finally available by default in all browsers on all platforms and on both desktop and mobile devices.

Scientific applications now have the ability to creatively communicate information in both 2D and 3D through HTML5 across all platforms and can be distributed freely over the internet. We have been making sure that WebGL support in the ChemDoodle Web Components remain compliant and thorough throughout its development. So no worries if you have not yet learned WebGL, as you can take advantage of this powerful 3D graphics technology for free under the GPL license through the ChemDoodle Web Components, joining hundreds of other projects that currently use our library to create the most stunning scientific web and mobile apps.

There is a demo of what can be done with ChemDoodle Web components in the hints and tutorials.


ChemDoodle 7 released


The latest update to the hugely popular chemical drawing package ChemDoodle has just been announced.

Some of the new features in ChemDoodle 7:

  • A new and improved interface based on the feedback from the last 6 years. The new interface is focused on the content and allows you to maximize your drawing areas. Widgets are now floating and can be individually enabled and disabled.
  • ChemDoodle 3D. A new application for creating 3D graphics and more for the sciences. You have full control over the 3D graphics and animations, including text. Distance, angle and torsion measurements are provided. Also a corresponding builder for 3D ChemDoodle Web Components. There is so much more.
  • Full multipage document support. Create lists of pages or grids. Draw between all pages and print them out.
  • BioArt. Large, full color, libraries of new art for use in biological figures, including animals, organs and organelles.
  • A set of 48 safety symbols included in the glassware set.
  • Significant performance improvements, in many cases 20x faster than v6. ChemDoodle will now load faster, work faster and respond faster.
  • New drawing features: collapse fragments to labels, incrementing list attributes (to quickly number or designate parts of structures), new TLC options, rotate atom labels if only a single atom is selected (as opposed to the global option), and more visual specifications among others.
  • Twitter integration.
  • Integration with the LabArchives ELN.
  • Support for both Java 6 and 7 on Mac OS X.
  • Dozens more improvements and additions.

If you want to find out more about ChemDoodle 7 there are a series of Webinars that describe it in detail

I hope to write a review later this week.


ChemDoodle Web Components Updated


The excellent ChemDoodle Web Components have been updated.

This is a bugfix update to the ChemDoodle Web Components, fixing all the issues brought to our attention. Fixes

  • WebGL based components now work in IE11.
  • iChemLabs Cloud services now work based on a queue, so all requests will proceed in the order requested, and you will no longer see a message to wait for the previous request to finish.
  • Added a iChemLabs.useHTTPS() function for websites that want only to use HTTPS.
  • Optimize zone now provides better placement when drawing triple bonds or higher.
  • Optimize zone now avoids placing substituents inside of rings.
  • Removed code calling jQuery.browser which was removed in jQuery 1.9. This code is only helpful for detecting when to use Google Chrome Frame. Note that Google Chrome Frame support (and therefore support in IE6-8) will be removed soon.
  • Fixed issue where clicking on the help button in some browsers would lock the component into a drag gesture.
  • Fixed bug where rendering atoms in 2D surrounded with a circle would error out.
  • Improved and simplified shaders.
  • Picking in 3D is now object aware, and will exclude objects if not selectable. So picking atoms for measurements is now much more responsive.
  • Fixed issue where measurements were not working in the Editor3D canvas on Android.
  • Help button now works in the Editor3DCanvas on Android.
  • Measurement values now render with a forward z-index of 1 â„«ngstrom to be placed on top of any objects in the immediate vacinity.
  • Minor syntax and lexical fixes.

There is a quick tutorial here, and many more on the ChemDoodle Web Components website


ChemDoodle Update


ChemDoodle has been updated to version 6.0.1, this is a free update to fix a couple of bugs.

  • A new EXE is built for Windows. This EXE will now use either the 64 bit or 32 bit JRE if available. If both are available, the new executable defaults to the 64 bit JRE.
  • iChemLabs Updater has been updated to work in mixed Java environments on Mac OS X. Those with both Java 1.7 and 1.6 installed on Mac OS X will notice that ChemDoodle will not automatically open after the update. Ignore this, as this new updater corrects this issue.
  • Fixed IUPAC naming issue where locants were not correct in ring blocks for stereocenters.
  • Fixed IUPAC naming where a double dash could occur.
  • Fixed bug where groups would not always resize all their contents.
  • Fixed crash if non-recognized colors were present in ChemDoodle Documents.
  • Colors in groups and reaction area text are now stored correctly in ChemDoodle Documents.
  • Limited the size of files previewed by the Quicklook plugin to 200MB.


ChemDoodle Web Components 6 released

iChemLabs have just announced the release of ChemDoodle Web Components 6, this is a major update to their javascript based chemical structure drawing and rendering package.

One of the most important changes from a developers point of view is the external libs (jQuery, jQuey UI, jQuery plugins, glMatrix) are now included into the ChemDoodle scope. This offers several advantages, including eliminating all library conflicts, reducing the number of files required to be installed, and controls the versions used by ChemDoodle. You can now include these libraries yourself at any version and not worry about conflicts. To use the libraries inside of ChemDoodle, call them from the ChemDoodle.lib closure. When I created the interactive graph using FLOT this was one of the issues.

There is also a new EditorCanvas3D canvas which is the 3D component allowing you to interact with and alter chemical data as the 2D Sketcher does in 2D. The 3D editor supports many new WebGL features including picking, highlighting and measurements (distances, angles and torsions).

Lewis Dot Structure style bonds can now be rendered.

As well as editing and drawing structures ChemDoodle web components provides an means to simulate NMR and mass spectra in a web browser

There are also a number of bug fixes and other improvements.

Please Note

This update includes some major refactors, such as the renaming of the sketcher files and packages and inclusion of the external libraries internal to the ChemDoodle scope, so pay careful attention when upgrading.