Macs in Chemistry

Insanely Great Science

Chemical drawing

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.


Roundtrip editing with ChemDraw 17.1


Whenever there is an update to ChemDraw I always hold my breath to see if 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) has been broken.

Fortunately this blog post provides an invaluable update to the current situation.


Molecular Materials Informatics Apps


Molecular Materials Informatics, Inc have been busy recently with updates to many of their applications

The following mobile apps have all been updated

PolyPharma Poly-pharmacology of molecular structures: use structure activity relationships to view predicted activities against biological targets, physical properties, and off-targets to avoid. Calculations are done using Bayesian models and other kinds of calculations that are performed on the device.

Green Lab Notebook allows recording of multistep chemical reactions, using molecular structure, name and stoichiometry as the primary components. When quantities are provided, interconversions are calculated automatically, and green chemistry metrics are shown.

SAR Table app is designed for creating tables containing a series of related structures, their activity/property data, and associated text. Structures are represented by scaffolds and substituents, which are combined together to automatically generate a construct molecule. The table editor has many convenience features and data checking cues to make the data entry process as efficient as possible.

MolPrime is a chemical structure drawing tool based on the unique sketcher from the Mobile Molecular DataSheet (MMDS).

Approved Drugs app contains over a thousand chemical structures and names of small molecule drugs approved by the US Food & Drug Administration (FDA). Structures and names can be browsed in a list, searched by name, filtered by structural features, and ranked by similarity to a user-drawn structure. The detail view allows viewing of a 3D conformation as well as tautomers. Structures can be exported in a variety of ways, e.g. email, twitter, clipboard.

Green Solvents reference card for chemical solvents, with data regarding their "greenness": safety, health and environmental effects.

For the desktop the OS X Molecular DataSheet (XMDS) is an interactive cheminformatics tool for viewing and editing molecular structures, chemical reactions and data. It is designed to be instantly intuitive to anyone who has used a Mac, a spreadsheet and any chemical structure sketcher.



The OS X Molecular DataSheet (XMDS)


The OS X Molecular DataSheet (XMDS) is an interactive cheminformatics tool for viewing and editing molecular structures, chemical reactions and data. It is designed to be instantly intuitive to anyone who has used a Mac, a spreadsheet and any chemical structure sketcher.

Its primary functionality is to provide a chemically aware spreadsheet editor: it operates on a grid of editable cells, made up of typed columns, that can be molecules, numbers or plain text, it also includes a chemical drawing app.


This is a significant foray into the desktop space for Molecular Materials Informatics who are best known for their excellent suite of tools for iOS, which includes the mobile SAR Table app and the Mobile Molecular Datasheet.


Nature Style guide for chemical structures


Nature have provided a style guide for drawing chemical structures

Although there are a number of ways that chemical structures can be drawn based on individual preferences, our journals aim to use consistent styling wherever possible.



A review of ChemDraw 17

ChemDraw is a very established chemical drawing package that probably set the standard for publication quality chemical drawing. However, on the Mac platform in particular I think it is true to say Cambridgesoft have taken their eye off the ball and released versions that were not up to their usual standard.

ChemDraw 17 is in someways a fresh beginning you can read the full review here.


ChemDoodle Web Components updated


iChemLabs announced the release of version 8 of the ChemDoodle Web Components, the largest update of the library to date. The ChemDoodle Web Components is an industry leading HTML5 toolkit for building scientific applications for web and mobile platforms. The ChemDoodle Web Components are licensed under the open source GPLv3 license or under a commercial license.


Executive Summary: Version 8 is the largest update to the ChemDoodle Web Components library to date. The sketcher has seen significant work, with new drawing tools (rings, chains, templates, atom label tool, more). Condensed labels with abbreviations are now supported, for advanced chemistry. New 2D shapes include dynamic brackets, atom mappings and variable attachment points, while molecular surfaces (vdW, SAS, Connolly) can now be generated and rendered in 3D components. The shader system used by the 3D components has been dramatically improved for much faster performance (and new improvements added like gamma correction) and a deferred shader has been implemented to provide advanced graphics techniques like outlining, software antialiasing and screen space ambient occlusion. Shadows can now be rendered in 3D scenes. The entire website has also been improved, with new advanced tutorials for working with the sketcher to listen to user changes, or show off an advanced in browser sketcher interface that mimics the desktop software, for instance. SVG can now be exported from the ChemDoodle Web Components in addition to PNG. A new iChemLabs Cloud service allows developers to match entire mechanisms for educational eBooks and advanced reaction databases. There is a lot in this update, please see the links below for more information.

New Features:

  1. The sketcher has been significantly developed. A new requireStartingAtom option allows you to disable to starting atom requirement while sketching. A new resizable option enables the user to resize the sketcher canvas. A new floatDrawTools option uses a floating toolbar for the drawing tools, just like the desktop software. Several new tools have been added, including an arbitrary ring size and arbitrary chain size tool. An atom label tool has been added with a text input field (like in the desktop software) to enter custom atom labels, including advanced condensed labels; space will open the text field by keyboard while the return or enter key will close it or repeat the last typed label for a hovered atom. Templates can now be added in the same manner as the desktop software using the new Templates widget; you can modify and add to the template library. The MolGrabber widget now allows the loading of any content (multiple molecules and shapes) and will insert the content in its entirety to the canvas. The MolGrabber widget will now also alert you if you press the Load button before the Show button. New buttons are available for centering the content in the sketcher as well as for horizontal and vertical flipping. The Open dialog now slides down from the toolbar as a Popover. The lasso tool and selections now use a dashed line just like in the desktop software. When using the labels tools in the sketcher, the periodic table canvas now selects oxygen by default and will revert back to label mode of the currently selected element if chosen from the toolbar. Silicon has been added to the default labels group. Placing unsaturated rings (like benzene) now better lay out double bonds to avoid overvalencing atoms. Hovering bonds are now more responsive, especially for elongated bonds. Pushers now can be set by clicking and then clicking again, no drag necessary.
  2. A new UIs component has been added, called Popover. A Popover is modal and can slide in from other components or appear in its own component for user input.
  3. Added mobile support for the UIs interface elements. For example, previously dialogs couldnt be moved on mobile devices, now they can.
  4. Complex labels can now be handled, with the required additional tools for parsing, formatting and rendering. With this feature, your chemical structures can contain advanced chemical labels consisting of element symbols, abbreviations (a dictionary controlled by you) and numbers and parenthesis for multiplicities. The labels are automatically formatted chemically and oriented based on least interference with surrounding bonds. Some examples include COOH, CO2Me, N3, CH2(CH2)4OH, C3H7O, Tosyl, myAbbreviation, and more. Use this to create concise publication quality figures directly in your websites.
  5. Added a wavy bond type.
  6. New shapes have been included. New 2D shapes include dynamic brackets for repeating groups, atom mappings for reactions and variable attachment points (VAPs). New 3D shapes include molecular surfaces. The ChemDoodle JSON specification has been updated to support these shapes.
  7. Molecular surfaces can now be generated and rendered for sets of atoms in 3D. Supported types include van der Waals, solvent accessible and solvent excluded (also known as a Connolly surface). You can control resolutions for all and the probe radius for solvent based surfaces. Rendering styles include Dots, Mesh and Solid and all colors, transparency, etc. can be controlled through visual specifications.
  8. The shader system for the 3D components has been redone. Several improvements in the Phong shader allow us to render higher quality graphics with lower quality meshes, leading to significant performance improvements across the entire 3D ChemDoodle Web Components.
  9. A deferred shader system has been developed allowing the implementation of advanced shader procedures for generating graphics. Currently implemented are outlining, screen space ambient occlusion (SSAO) and software antialiasing (FXAA). SSAO in particular is very powerful as it allows us to simulate how much ambient light is accessible to objects in crowded spaces, allowing us to shade the scene in a more accurate manner. This works on all geometries, but the feature can really be shown off in space filling all-atom models of large macromolecules.
  10. Shadows can now be rendered in 3D scenes. You can control the intensity of the shadows with the shadowintensity3D visual specification.
  11. Gamma correction has been implemented for brighter, more color accurate rendering controlled by the gammaCorrection_3D visual specification.
  12. The VisualSpecifications class now provides a copy() function for creating style sheet copies.
  13. Added a new bond visual specification for absolute saturation widths: bondsuseAbsoluteSaturationWidths2D.
  14. Bonds now split colors based on their substituent atom colors, with the bondssplitColor visual specification. The bondsuseJMOLColors and bonds_usePYMOLColors specifications have been removed. Use the corresponding atom specifications instead.
  15. Made wedge width an absolute value in line with desktop software with a default value of 6.
  16. Components now center 2D content much more pleasantly by calculating bounds of atom labels in addition to coordinates and using a constant internal padding.
  17. The preview, hover, select and error colors are now controlled by visual specifications.
  18. A new iChemLabs Cloud call, mechanismMatch(), is now provided to match mechanisms. You can see it in action here.
  19. Updated van der Waals radii data.
  20. Added the rest of the new elements as defined by IUPAC.
  21. Updated the library to use some newer standardized HTML5 functions, removing the polyfills from the ChemDoodle.extensions package.
  22. The PNG package has been refactored to provide both an open() function for loading the PNG into a new window and a string() method for creating a string object of the PNG content.
  23. A new SVG package has been added to create Scalable Vector Graphics data from the ChemDoodle Web Components, similar to the PNG package for bitmap graphics.
  24. Minor graphical improvements for the UIs decorations.
  25. Updated jQuery to version 2.2.4. Updated jQuery mousewheel to version 3.1.13.
  26. Updated the entire website. Added more advanced tutorials: Image Export, Initializing Components after Closing the DOM, Sketcher: Application Window, Sketcher: Listening to User Changes.

Full details of the update


SketchEl 2


As highlighted recently SketchEl2 a chemical drawing package is now open source.


The SketchEl 2 project is underway as a desktop app, based on web technology and delivered as an Electron package. The GitHub repository is now public, on account of there being enough functionality to be arguably useful. This is a very early release, so do be ready to give some useful feedback if you feel so inclined to try it out.

The repository can be found here


ChemDraw Innovation Challenge


Perkin-Elmer have just announced the ChemDraw Innovation Challenge - a forum designed to shape the future of Chemdraw

For the past 30 years, ChemDraw has been known around globe as the premier chemical drawing tool for chemists and biologists alike. While each version has brought more powerful features (many of which came from feedback from our passionate user base), we’ve all had that moment where we wanted ChemDraw to do [X]. We want to hear your ideas, suggestions for new features, new third-party applications we should integrate and more. The sky's the limit - big or small, all ideas are welcome!


Molecule Viewers and sketchers for iOS


With withdrawal of ChemDraw and Chem3D from iOS I thought it might be of interest to highlight some of the alternatives.

Put together two pages.

Molecule Viewers for iOS


Chemical Sketchers for iOS


iPad iOS apps - ChemDraw, Chem3D and CDSL have been withdrawn


PerkinElmer have announced that their iOS apps have been withdrawn.

Although PerkinElmer Informatics remains committed to making ChemDraw available to chemists everywhere, the iPad iOS apps ChemDraw, Chem3D and CDSL have been withdrawn from the Apple iTunes store effective immediately. The related Flick2Share capability is also withdrawn from service.

Whilst it was reported that there were plans to build an Android version in 2014 nothing has seen the light of day. It seems they are now focusing on ChemDraw Cloud.

If you already have ChemDraw or Chem3D installed they will continue to operate but the "flick2share" option will not function, it is unlikely that existing apps will be updated or supported in the future.

Alternatives for Chemical Drawing

There are a number chemical drawing apps alternatives to ChemDraw under iOS on the MobileScience Website. Perhaps the most popular is ChemDoodle Mobile and is provided to you for free when you purchase ChemDoodle desktop.

There are five main windows: Draw, 3D, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The 3D window allows you to view the drawn molecule in 3D. The Calculate page calculates properties and the Spectra page simulates NMR spectra. All spectra are interactive.

Elemental is a free chemical drawing app from Dotmatics. This is actually the same chemical sketching application provided for all the Dotmatics products and as is used for drawing chemical queries in ChemSpider. It is also used int ElementalDB an iPad app that demonstrates substructure searching the 1.2M structure ChEMBL database locally on your iPad.

Molecule is a simple modern chemical structure editor. Allow to draw and share chemical structure. MF, MW, Monoisotopic Mass and Elemental Composition calculated interactively during drawing.

MolPrime+ is a chemical structure drawing tool based on the sketcher from the Mobile Molecular Datasheet from Molecular Materials Informatics, Inc. It provides a way to view and edit chemical structure diagrams on an iPhone, iPod or iPad. The unique and innovative sketcher is optimized for the touchscreen interface, and allows professional quality molecular structures to be drawn quickly and efficiently. The same drawing tool has been used in the Green Lab Notebook.

iMolecular Draw is an application that can view, edit and build molecules in 2D.

Chirys Draw chemical drawing app for publication-quality molecular structures and reactions. Designed from the ground up for the iPad, Chirys Draw takes advantage of unique multi-touch capabilities to make drawing molecular structures and reactions easy and accurate.


ChemOffice and ChemDraw version 16.0.1 released


I just noticed that a new version of ChemDraw has been released.

ChemDraw and ChemOffice 16.0.1 provides a point release to address a number of usability concerns, primarily on Mac, identified subsequent to the 16.0 release. ChemOffice Pro, ChemDraw Pro, ChemDraw Prime and the ChemDraw Active-X control (CDAX) have been updated.

I have no details on what issues have been addressed, hopefully the topic on the Cambridgesoft forum will provide more user experience.

Forum Topic:- Update Chemdraw 16 Mac


SketchEl2 Chemical Sketcher


A new chemical drawing app SketchEl2 has been released.


It is based on the an original java app but as the author notes.

Although a few holdouts may disagree, Java is not the platform of the future for the desktop (that ship sailed a long time ago).

So the new version SketchEl2 is now a web runtime app built using the Electron Framework) and Node.js and the Chromium web browser.


OSRA 2.1.0 released


Just got this email

I am glad to announce the release of OSRA 2.1.0. OSRA (Optical Structure Recognition Application) is a tool for converting images of molecules into SDF, SMILES and many other chemical formats. Images can be pictures of single molecules or complete PDF documents with multiple pages of text and graphics. In addition to molecules OSRA can also recognize reactions, and, starting with this version, simple polymers.

The improvements in this version: - Significantly improved recognition of PDF documents, no longer dependent on Ghostscript at runtime. - Recognition of polymers (different approach from POSRA - a separate tool focused on polymer recognition).

The new version is available at

Please note that if you are building from source the dependencies have changed. OSRA now requires poppler (version 0.41) to process PDF files and a custom-patched version of OpenBabel to save polymer MOL and SDF files. The patched version of OpenBabel is provided at the above url. OSRA no longer requires Ghostscript to be installed.


ChemDraw 16 Review


There is a review of ChemDraw 16 over on Chemistry and Computers.

A key feature is found-trip editing, wherein a user could make a drawing in one application, copy and paste the drawing into another application, and then later copy and paste back into the original application, and still be able to edit the drawing. Generations of Mac users relied on this feature to go from applications like ChemDraw into PowerPoint and back again. This has been has been regularly broken as we had various updates to Mac oSX, Microsoft Office, iWork and ChemDraw. It sounds like some interoperability has returned but it may depend on which versions of the various components you are running.

Now updated to include Mac OSX Sierra, ChemDraw 16 works and round-trip editing using Word 2011 still works! Unfortunately round-trip editing appears to be broken in Pages, Keynote and Numbers.


ChemDraw 16


I see a new version of ChemDraw has been released. The flyer suggests improved Mac support

ChemDraw 16 for Mac is 6x faster than previous versions and includes features such as: auto-save and versioning, an improved UI, Unicode support, Improved text rendering including for subscript characters and atom labels. What’s more, ChemDraw 16 for Mac offers improved multi-monitor and Retina (high DPI) display support.

Requirements are shown below, no mention of Mac OS X 10.12 (Sierra)

Following are the system requirements for the latest version of ChemDraw.


  • Mac OS X 10.10 (Yosemite)
  • Mac OS X 10.11 (El Capitan)


  • 32 bit OS: 1 GB
  • 64 bit OS: 2 GB

Microsoft Office

  • Microsoft Office 2011
  • Microsoft Office 2016
  • including Office 365 support

Initial comments suggest round-trip editing is now supported. No mention of Pages, Keynote, Open Office.


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 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.

Finding Duplicate structures


It is always interesting to note which scripts attract the most attention, often it is scripts that aid with relatively simple tasks. Among the Applescripts it is the script to simply print the clipboard.

Recently I wrote a script to remove duplicate structures from within Vortex

When working with multiple data sets of molecules, particularly if combining them from multiple sources, one of the most common tasks is removal of duplicates. This can be a time-consuming and error prone process if carried out manually and this script should hopefully make this a much easier task.

This seems to have attracted interest but I got a comment that it "works fine but is slow for larger data sets". So I've been looking at improving performance.

In order to test the performance I took around 150,000 random structures from ChEMBL and then duplicated 0.01% to give a test set of 160,146 molecules. The original version of the script took 95 mins, using the same test set, version 2 of the script took less than 3 mins! This increase in performance means that it is now practical to use the script on much larger datasets.

You can read full details and download it here.

There are many more Hints, scripts and tutorials here.


ChemDraw 15.0


At long last ChemDraw for Mac has been updated. The latest version now supports Mac OS X 10.10 (Yosemite) and supports the retina display.

Whereas in the past we had Std, Pro and Ultra we now have Prime and Professional and cross grades are available.


A reader just sent me the official ChemDraw 15 feature chart

The ability to search SciFinder is now available in ChemDraw Professional Mac version, and the only differences are lack of OLE editing, and the absence of the pKa LogP LogS calculations.


Scientific Applications under Yosemite


I just thought I'd like to thank all those who contributed to the Scientific Applications under Yosemite web page, many users and developers contacted me either via email or in the comments section and they certainly added information about applications that I don't have access to.

To date the page has been viewed well over 10,000 times with readers from 188 different countries. Viewers spent an average of just under two minutes on the page and it still attracts 800 pages views a month.

Given that 75% of the visitors to the site are now using Yosemite I suspect most scientists have now made the transition and I won't be updating the page any more. Once again thanks for the contributions.


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 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


I just got this email

ChemDoodle 7, released in September, continues to receive great reviews and an ever increasing userbase in over 80 countries. We are working hard on many new features and continue to improve the massive number of features already available. We want to let you know that introductory pricing ends on December 31st, 2014. If you have friends or colleagues who are considering purchasing ChemDoodle, please tell them to purchase by the end of this year to take advantage of these low prices, and save as much as 50% off the regular price.

You can buy ChemDoodle here:

There is a review of ChemDoodle here.


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.


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.


ChemAxon 6.3 released


ChemAxon have just announced the release of version 6.3.

This release includes several new features including the ability to draw and analyze complex patent Markush structures, display Markush hierarchy, work with R-Groups and enumerate Markush structures.

A new Solubility Predictor, the aqueous solubility predictor is based on the topology of the input molecules, but also calculates the pH dependence and the solubility at a desired pH level.

IUPAC name conversion supports now Japanese names as well as the existing English and Chinese names even if mixed in the same document so you can extract all the chemistry from documents in these languages.

There are also updates for Marvin JS 6.3, Standardizer & Structure Checker 6.3, Instant JChem 6.3, and Compound Registration 6.3.


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.


A first look at ChemBioDraw 14


ChemBioDraw 14 was released recently and I thought I’d download the demo version and have a quick look at it. I’ve written my first impressions here.


ChemPencil and ChemEquate


ChemPencil is an inexpensive chemical drawing application that has all the usual chemical drawing tools. However as fas as I can tell it does not currently support round-trip editing, structures are pasted into documents as images and can not be then copy and pasted into ChemPencil for further editing.

There is a listing of some chemical drawing apps here and a review of ChemDoodle here

There has been an update to ChemEquate automatically formats and balances chemical equations. Copy with one click for use in word processing applications. Molecular weights are also conveniently provided.


Survey on ChemBioDraw

Perkin Elmer are looking for input on ChemBioDraw

Calling all chemists! PerkinElmer wants to know what changes you would like made to the #ChemDraw ChemOffice suite? What features are important to you? Which ones are needed? Which ones do you never use? Please help us design the future direction of this product by completing this short (1 page) survey

Given the comments I’ve received from readers this seems like a chance to at least get your views registered and ask for better Mac support.


Elemental updated


Shortly after announcing 100,000 downloads Dotmatics have posted an update to the chemical drawing app Elemental for iOS.

  • Interface tweak for iOS 7

Previous improvements - iOS 7 update - Elemental drawing bug fixes - Property prediction bug fixes - iPhone 5 support - Updated predicted properties engine - YouTube video link for introduction to the app - App size reduces from 8MB to 1MB(!) - Dropbox and Twitter Integration - Calculated Properties Panel - Rate Elemental Button! Love Elemental? Please rate us! - Follow us on Twitter button - @ElementalApp - Full Retina Display Support - File association improved - Sketched molecules persist over restarts - Copy image to Camera Roll - Copy Image to Clipboard - File association (tap and hold to load in Elemental) - E-mail attachments have been improved - support for multi-centre bonds added - Multitouch gesture support Undo - double tap Zoom - pinch Scroll - two finger drag - E-mails now export a reaction/RXN file if the sketch contains an arrow - MOL file e-mails contain predicted molecular properties: MW, MolFormula, XLogP - Add text notes into your sketch - Now compatible with iOS 5.0 and up - E-mailing of images has been improved - Larger icons

There are many other Chemical Drawing Apps that support iOS


Elemental for iOS


Dotmatics have just announced that the chemical drawing app Elemental for iOS has been downloaded 100,000 times. Whilst not in the same league as Angry Birds it surely marks an important milestone for scientific apps for mobile devices.

There are many other Chemical Drawing Apps that support iOS


Still waiting for an update?


At the WWDC on June 10 2013 Apple announced the latest version of the Mac OSX operating system and on the following October 22 they announced it was available as a free instal from the Mac App Store. Since then there have been two updates leading to the current 10.9.2.

As soon as the update was announced at the WWDC many software companies started checking and updating their software so that when Mac OSX 10.9 was released they had compatible updates available immediately or shortly after. I kept a list of scientific applications under Mavericks and have updated the list periodically. Most software is now compatible, or there are workarounds. However recently I was made aware of the situation with ChemBioDraw from Perkin-Elmer (formally Cambridgesoft). ChemBioDraw has been a major chemical drawing package on the Mac for as long as I care to remember however the current version is not compatible with Mavericks. Indeed when you look at the support forum there are reported issues with retina display dating back to 2012! A support topic that has been viewed nearly 6000 times but not yet fixed apparently. There are many comments of the support forum but perhaps this gives you a flavour.

I confirm, the copy/paste issue in Mac version of ChemDraw 13 makes it totally unusable!!!! I suggest this is not only a problem with the compatibility with Mavericks. It never worked in Mountain Lion too! This issue is at least one year old and the developers just continue to ignore this issue. ChemDraw 13.0 crashes >90% of the time when you copy/paste a structure.

As of writing there is no indication when there will be a fix or whether earlier versions of ChemBioDraw will also be updated. This software is very expensive $1140 for a one year license! So my question is what is a reasonable length of time to expect to wait for an update?


Marvin updated


Marvin has been updated to version 6.2.1


Marvin 6.2 released


Marvin 6.2 from chemAxon has been released.

This is a major update and the release notes can be found here, of particular note are

  • TIFF AND EPS FORMAT SUPPORT: Chemical structures can be exported to TIFF or EPS image formats in MarvinSketch and MarvinView
  • R-GROUP DISPLAY AND EDITING: In MarvinSketch editing and displaying R-groups were modified and improved in several cases.
  • COPY – PASTE BETWEEN MARVINSKETCH AND MARVIN FOR JAVASCRIPT: Structures can be copied from and to the canvas of our Java based MarvinSketch and Marvin for JavaScript .
  • R-groups added to Marvin for JavaScript: R-group definitions can be created and edited; and attachment points can be added to a structure
  • Chinese Name to Structure: Frequent OCR errors in Chinese characters are now corrected automatically

3D structures in javascript


Several sites are now using javascript rather than java plugins to render 3D chemical structures, ChemTube 3D contains interactive 3D animations and structures, with supporting information for some of the most important topics covered during an undergraduate chemistry degree.

ChemTube3D news - 2014 version uses Javascript and so works on iPads. It is slower but less problematic than Java. Please use latest versions browsers for best results.

Henry Rzepa has used his blog to offer insights into reaction mechanisms. However the issues of security have made the use of java plugins an onerous task to maintain. His solution:-

Replace the use of Java applets with one not dependent on Java. In the last 18 months an amazing effort to do this has resulted in JSmol, which uses only JavaScript (which has nothing to do with Java despite the name).

I see more and more sites using the javascript and HTML5, recently we have see and update the ChemDoodle Web Components, I suspect all chemical drawing packages will need a javascript version in the future for both 2D and 3D rendering.


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.


Marvin 6.1.5 has been released

Marvin has been updated

Bugfixes, Java Webstart did not run on Macintosh computers.

It can be downloaded from here

Note, many of you have bumped into the problem when the Gatekeeper Security of OS X blocks launching applications downloaded not from the Apple store. The solution is to modify the default settings of the Gatekeeper:

  • 'Apple > System Preferences > Security & Privacy '
  • In the 'General' section the setting of ' Allow applications downloaded from :' should be set to ' Anywhere'

After this you would not get the "damaged dmg" popup and you can install the downloaded dmg. After install it is probably a good idea to reset the Security settings.

If you are using Java applets it is probably worth reading this article

Apple just have introduced some new security settings in Safari for Java. In an average browser to make  a Java Applet to be able to touch your file system that Applet must be signed. In the new security update of Safari this Applet must be trusted as well. This means that you have to allow for the Applet to read and write you file system. Marvin starts with accessing some files on your computer, which means that it might not start without this permission or might not behave correctly


Export as mol file


A number of publishers are seeking to add extra value to publications by including access to chemical structure information to aid searching and indexing. More details are included in this comment from Elsevier.

Elsevier would like to enrich online articles by visualising and providing details of chemical structures you define as the main chemical compounds described in your article. For this purpose, mol files of the key compounds can be uploaded in EES. Please use your preferred drawing tool to export chemical structures as mol files and ensure that they are well defined and do not contain aromtic bonds, R-Groups or other variables. Submitted mol files will be available for downloading from your online article on ScienceDirect. Furthermore, Elsevier will generate InChI keys from the mol files and include them in the online article, which increase the online searchability of your article e.g. in Google. InChI keys will also be used to link the article to additional data in Reaxys.

Since you need to export each structure as an individual file this will become somewhat tedious, fortunately Brian Myers has written an applescript that greatly helps the process for ChemBioDraw users

Now updated.


ChemDoodle 6 released

The latest update to the increasingly popular chemical drawing package ChemDoodle has just been released. ChemDoodle 6 is the latest update from iChemLabs and once again it supports Mac, Linux and Windows and works with most document creation packages. This is apparently a free upgrade for those who recently purchased ChemDoodle 5. I plan to write a review of ChemDoodle 6 when I have time but looking at the release notes this looks to be a substantial update.


New features in ChemDoodle 6:

  • IUPAC naming with over 20 options!
  • Carbon nanotube and prism builders. Both zigzag and armchair nanotubes can be built. These tools quickly produce 3D geometries.
  • Auto updating labels can now be attached to molecules, so they will update with IUPAC names, molecular formulas and more.
  • Mac OS X Quick Look plugin. Easily preview all your chemical files in Finder just by pressing the space key.
  • More Windows support, including a more powerful tool for supporting Windows filetype associations with the option to unassign types, support for the MDLCT and MDLSK clipboard formats for copying and pasting between a wider array of chemical applications, and greatly improved OLE support to allow for double-clicking to edit structures.
  • More glassware, including a new organized glassware window. You can now also remove liquid from the templates.
  • Significantly improved graphics. Graphics in ChemDoodle were already very good, but we took a look at all the graphics at very high scales and resolutions. We have made sure to focus on all the little details. Bond join edge cases have been improved. Hashes are now auto centered, making recessed bonds and dashed bonds look much nicer. Other bond types have been scrutinized for the best aesthetics. Convex hull algorithms have been built for better placement of bonds around labels. Cis double bonds will now prefer the inside edge. Circles over charges now only surround the number. Aromatic ring circles now meld to the shape of aromatic circles. Arrows look nicer. You won't find better graphics in any other application.
  • 3D coordinate generation.
  • A new 180° chain angle clean option for easily creating Lewis structures and figures with 90° angles.
  • Complex embedded ring systems (like corannulene) now clean very well in 2D.
  • Added resolution controls to the Elemental Analysis widget.
  • Meso stereochemistry support.
  • An advanced formatted text system for the system clipboard. You can now copy and paste your molecular formulas, IUPAC names and others into word processing applications with formatting intact.
  • Many other minor, but useful features: option for the delete key to decrement bonds, nominal mass counter, improvements to the TLC Plate widget, improvements to arc placement previews, alt and shift now modify attribute placement just like placing bonds, improved file chooser previews for data files, more templates for the Templates widget, and more.
  • Squashing of dozens of bugs.

Remember also that there are also ChemDoodle Mobile.

ChemDoodle Mobile, the mobile companion to ChemDoodle, is provided for free to ChemDoodle desktop customers. ChemDoodle Mobile is available for both iOS (iPod Touch/iPhone/iPad) and Android devices. You can transfer structures between ChemDoodle desktop and ChemDoodle Mobile, to take with you into the lab


Chem3D and ChemDraw for iPad updated


Both ChemDraw and Chem3D have been updated, the release notes don’t give much information on the updates other than Redesigned for iOS7 and bug fixes.

The use of mobile devices in teaching has offered new opportunities and a recent presentation by Layne Morsch illustrates this quite nicely. Using ChemDraw for iPad and Flick-to-Share to Increase Engagement in Organic Chemistry. The page has a couple of embedded videos that give more details.

The other feature that is now becoming mainstream is the 3D-printing and since Chem3D can export in .stl format it is not surprising people have started to experiment with creating 3D models of molecules, there is a brief video here, unfortunately it is a loop of the printing process so don’t expect to see the final product. CambridgeSoft have also produced their own videos of these apps in action


Bug in ChemBioDraw.


There was a blog entry on In the Pipeline about a bug in ChemDraw. Actually this has been known for a while (and present in previous versions) but it seems it still has not been fixed in the latest version of ChemBioDraw 13 on the Mac. As you can see in the image below including explicit hydrogens in your structure significantly impacts the calculated LogP. Whilst people don’t often add explicit atoms to phenyl rings, (expect perhaps in SAR studies) they often add them to heteroatoms.


At the moment there is no bug fix and no date set for a fix to any version of ChemBioDraw, the only approach is to avoid adding explicit hydrogens to structures if you want to calculate LogP. I’ve looked at a number of other applications and there seem to be no issues with ChemDoodle, Elemental, Marvin or OpenBabel.


Marvin 6.1.3 released


ChemAxon have released a new update to Marvin.

Bugfixes MarvinSketch GUI MSketchPane setPiece(Molecule) method did not work, it set the molecule on the canvas instead of putting it on the cursor. Import/Export CXSMILES/CXSMARTS CXSMARTS containing valence property information was recognized and read as SMARTS. SKC Some reaction was read as R-definition from SKC format.


Marvin 6.1.2 released


New features and improvements

  • MarvinSketch Dialog
  • 'Zoom to scaffold' checkbox option has been added to the "Preferences>Save/Load" tab. Documentation
  • Structure Checker
  • External structure checker configuration file URL can be set via Java System Property.


  • Editing
  • Electron-flow arrow could not be drawn from the A-B bond to the incipient A-C bond of an A-B-C structure. Forum
  • Import/Export
  • MolInputStream and MolImporter could have different format options.
  • MolImporter did not close its inputstream when an exception was thrown in the constructor.
  • Molecule type property was allowed in SDF, CSSDF export.
  • The coordinates of the sequence residue imported from SCSR MOL files were wrong if the residue had three attachment point.
  • Color and text format of atom label is exported to CDX and imported from CDX and CDXML. Forum
  • Graphical brackets were not imported from CDX files.
  • Gaussian Z-matrix input format
  • Command line, title line, and extra input properties were not exported to Gaussian Z-matrix input format. Forum
  • Clean 2D
  • Cleaning of position variation bonds could create overlapping bonds.
  • Cleaning of bridged systems could result in overlapping atoms. Forum
  • Calculations
  • Topology Analysis
  • Missing method has been added: TopologyAnalyserPlugin.getFsp3(). API Documentation
  • logD
  • New logD training documentation has been added. Documentation
  • Structure Checker
  • Fixer options in MarvinSketch are updated with newly defined settings.
  • External checkers can be loaded from JAR file in case the JAR file contains a space.

Marvin 6.1 has been released

Marvin 6.1 has been released:   New drawing and displaying features in MarvinSketch and MarvinView
Among others drawing peptid cycles and bridges is available now, and IUPAC numbers can be displayed in MarvinSketch and MarvinView
Better images to structures conversion in Document to Structure
Optical Structure Recognition tools CLiDE and Imago can be used, in addition to OSRA
New Chinese Document to Structure feature
Chemical names in the flow of Chinese sentences are detected, without the spaces that separate words in English
Marvin for JavaScript news
Homology groups has been added Structure Checker got an integral part of Marvin Beans
Installing Marvin Beans will install the fully functional Structure Checker application

  • Structure Checker: Checker names and error messages can be localized or customized
  • Elemental Analysis: Charge is taken into account in atomic mass calculation
  • Structure Checker: “Copy as action string” option is available


ChemDraw and Chem3D for iPad updated

I just noticed that there are a couple of updates on my iPad, in particular ChemDraw and Chem3D for iPad have both been updated. What is particularly appealing is that they certainly seem to be listening to their users with several of the top requested features now being incorporated. I’m particularly delighted to see DropBox fully integrated as a sharing capability, for a mobile device this is absolutely critical. At the moment you can upload CDXML, PNG or PDF file formats, and you can only save to a ChemBioDraw folder within DropBox. Perhaps unsurprisingly social media outlets (Twitter and Facebook) are now also supported.

Chem3D now has the ability to pull more structures from public databases, perhaps in the next update of ChemDraw we might see the ability to pull structures from public databases such as ChemSpider?

The ability to add text boxes to structures and schemes will be very useful and will make this a more useful app for note taking. The default text seems to be Times New Roman but you can change text style using the “Colours and Styles” button. The ACS template is now available, but you can’t use your own templates.

ChemDraw for iPad 1.0.2 Features

  • Text capability to annotate structures and reactions (single-most requested feature in product reviews)
  • Adjustable arrows (another top requested item)
  • More sharing capabilities including DropBox, Twitter, Facebook, and Moxtra
  • Group Flick-to-Share (based on our summer pilots and geared toward educators)
  • Orbitals, brackets
  • Two categories of templates (structures)
  • Enhanced periodic table keyboard capabilities including an ability to quickly type a chemical formula
  • American Chemical Society template
  • Simplified Chinese language support
  • Korean language support   Chem3D 1.0.2 Features

  • More sharing options including DropBox, Twitter, Facebook and Moxtra

  • Ability to pull in more structures (PDB and CIF) from public databases including now by keyword search for structure or author
  • Group Flick-to-Share capabilities
  • Simplified 3D printing output (now via DropBox or email)
  • Simplified Chinese language support
  • Korean language support

These are excellent updates and well worth installing. A minor comment since Chem3D can import PDB structures from public databases, it might be nice to be able to save them in PDB format.

I’ve updated review I wrote.


Marvin for Javascript

The Marvin package has been updated to include Marvin for Javascript and has been released. It is a light-weight chemical editor suitable for generating standard chemical structures and simple queries on modern web browser pages without the need for installing Java. It provides all the essential features for quick and easy structure drawing as well as flexible editing options for molecular manipulations


Marvin Update

New features and improvements
Image I/O
The following file extensions were removed from the "Files of Type" list on the Import Image dialog: *.ps, *.pdf, and "All Files".
PDF files can be imported through the "File > Open" menu.
Calculation Services
SOAP version 1.2 webservices are supported.

There are a number of bug fixes.

On the Mac clipboard handling has been improved, On Mac OS X, copy-paste (from MarvinSketch to, e.g., TextEdit) did not transfer the atom colors.


ChemDoodle Updates

IChemLabs have announced a couple of updates

ChemDoodle Web Components 5.2.2 has been released, this is a minor update This update fixes some issues, and most notably stabilises the WebGL text system. They have updated a few of the demos to show off this feature:

2D to 3D Coordinates
MolGrabber 3D
PDB Ribbons

ChemDoodle mobile 1.4.1 is also now available from the App Store, the release notes include.

  • Support for the iPhone 5
  • IUPAC Naming
  • 3D coordinate generation and viewer
  • Added empirical formula to calculations
  • Added rotatable bond count to calculations
  • Added total electron count to calculations
  • Added vdW volume to calculations
  • Added complexity to calculations
  • Fixed slow performance issues on iPad in landscape mode
  • Fixed MolGrabber search issues
  • Fixed issue where the back button wouldn’t appear on the last help page
  • Fixed login issues
  • Performance improvements
  • General improvements and fixes


ChemDraw for iPad

About three decades ago I stopped using a stencil and a Rotring pen to create chemical structures for publications and started using ChemDraw on a Mac, at the time it transformed the standard of structures in publications and it has continued to set the standard for publication quality chemical structures. Over the years the software has developed and moved into cheminformatics, spectroscopy and more recently biological drawing. This lead to the rebranding as ChemBioDraw but most of the chemists I know still call it “ChemDraw”. So it is perhaps not surprising that I feel rather pleased that the iPad version is entitled simply ChemDraw.

You can read a full review here.


ChemAxon Update

ChemAxon have announced an update to their desktop suite of applications.

Version 6 for scientists:

  • All GUIs are refreshed to simplify both the user experience and access to key chemistry functions
  • Marvin for JavaScript – new light-weight chemical editor for web pages which does not require Java
  • Plexus – new web-based application for medicinal and computational chemists, featuring dynamic data visualization,

MacOSX 10.8 users should also note this support message

Many of you have bumped into the problem when the Gatekeeper Security of OS X Mountain Lion blocks launching applications downloaded not from the Apple store. The solution is to modify the default settings of the Gatekeeper:

  • Select 'Apple > System Preferences > Security & Privacy '
  • In the 'General' section the setting of ' Allow applications downloaded from :' should be set to ' Anywhere'! After this you would not get the "damaged dmg" popup and you can install the downloaded dmg. You even don't need to re-download it, the "damaged dmg" is misleading.


JSME: a free molecule editor in JavaScript

Another javascript-based molecular editor JSME was recently described in the Journal of Cheminformatics, JSME is a port of the very popular JME java applet.

The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages.


OSRA Updated

OSRA 2.0.0 is available for download.

OSRA (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures and reactions, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or MOL files –

  • Significantly improved recognition rates. Full details of the validation are available.
  • Added recognition of Iodine, wavy bonds, etc.
  • Completely modified confidence function (values not compatible with the earlier versions).
  • Updated table detection and removal routines.
  • Created binary package for Linux (statically linked, should work on all modern Linux systems).
  • Windows and OSX versions now support multi-threading processing of PDF files.

With this release the distribution model has been changed a bit: while the source code is available free as before, to offset the development costs the installable packages for Windows, Mac OSX and Linux can be purchased for a fee.


Software from Open Chemistry

The Open Chemistry Group have just announced the availability of the first beta release of a suite of software packages for chemists.

It consists of Avogadro 2 an update to the well established molecular editing package, see a recent paper describing it for more details “Avogadro: an advanced semantic chemical editor, visualization, and analysis platform” DOI.

Some notable new features of Avogadro 2 include:

  • Scalable data structures capable of addressing the needs of large molecular systems.
  • A flexible file I/O API supporting seamless addition of formats at runtime.
  • A Python-based input generator API, creating an input for a range of quantum codes.
  • A specialized scene graph for supporting scalable molecular rendering.
  • OpenGL 2.1/GLSL based rendering, employing point sprites, VBOs, etc.
  • Unit tests for core classes, with ongoing work to improve coverage.
  • Binary installers generated nightly.
  • Use of MoleQueue to run computational codes such as NWChem, MOPAC, GAMESS, etc.

The second component of the suite is MoleQueue, a new tool to manage and execute computational tools either locally or on a remote machine or cluster. The messages transmitted between the client and server are formatted use the increasingly popular JavaScript Object Notation (JSON) format and adhere to the JSON-RPC 2.0 specification.

The final element of this first beta release is a chemically aware database MongoChem built on MongoDB intended to address the need for researchers and groups to be able to effectively store, index, search and retrieve relevant chemical data. It uses Open Babel to provide the cheminformatics input

There is a slide presentation describing the project in more detail here/


A couple of Updates

Marvin 5.12.3 has been released with a couple of bug fixes


  • Name to Structure (n2s)
  • Names with ylium and uide suffixes are now supported.

Calculation NMR (HNMR, CNMR Prediction, ...)

  • Coupling of a nucleus with a group of magnetically equivalent nuclei was not handled properly.
  • NMR Predictor did not consider negative coupling constant values.

JSDraw has been updated as part of the Cheminformatics DevSuite 2.5.1 Release.

There is an online demo of 3D structure generation here using JSME and JSmol.


ChemDoodle Mobile Updated

I just noticed that an update for ChemDoodle was available on my iPhone.

According to the release notes this includes

  • Support for the iPhone 5
  • IUPAC Naming
  • 3D coordinate generation and viewer
  • Added empirical formula to calculations
  • Added rotatable bond count to calculations
  • Added total electron count to calculations
  • Added vdW volume to calculations
  • Added complexity to calculations
  • Fixed slow performance issues on iPad in landscape mode
  • Fixed MolGrabber search issues
  • Fixed issue where the back button wouldn’t appear on the last help page
  • Fixed login issues
  • Performance improvements
  • General improvements and fixes

There is a page of mobile science applications here.


Marvin Updated

Marvin 5.12.2 has been released with a couple of bug fixes

Molecule Representation

  • Conversion from explicit hydrogen to implicit one removed stereo centers not having explicit hydrogen ligand.


  • Non ring bond information were imported as query strings from SMARTS.
  • After SMARTS import, those atoms that had no explicit aromatic property but had aromatic bond got query aromaticity property.


Marvin 5.12.1 released

New features and improvements


S orbitals and oval shaped s or p orbitals are imported from CDX/CDXML.


Painting, Charge symbol on carbon atoms was missing when the atom numbers were visible and the display of carbon atom labels was turned off. When two atoms had more than one electron flow arrows between them, the electron flow arrows overlapped each other. The second electron flow arrow started from a wrong position when a single electron and an electron pair flow arrow started from an atom which had a lone pair and a radical as well.

Editing, Atom Lists and NOT Lists could not be created by typing atomic symbols separated with commas (e.g., "f,br,cl" or "!f,br,cl").

Import/Export, MRV and CML export wrote out characters incorrectly which are not supported by the character set. SDF files having invalid header could not been imported. Deuterium and tritium isotopes were converted to simple hydrogen atom if a molecule was exported to ChemAxon compressed MOL format (CSMOL). MolExporter.exportToObject() added an extra newline to SMILES. Nitrogens connecting two aromatic rings had radical after import if nitrogen was bracketed in the SMILES representation. Absolute stereo flag was missing during InChi export/import and InChiKey export.

Molecule Representation, Number of added implicit Hydrogen atoms were incorrect in some cases for positively charged sulfur atom.

Calculation, After canonical tautomer generation, the information of "double cis or trans" bond type might have been lost in certain cases.


Publication Quality Chemical Structures

There are two main occasions when a chemical drawing package is needed, firstly as a front-end to a chemical database for creating structure-based queries, and secondly for creation of chemical structures in publications. Whilst many drawing packages are fine for query construction some are far from ideal for creating publication quality output.

This paper from Alex Clark (DOI: 10.1002/minf.201200171">10.1002/minf.201200171) discusses the issue in detail.

The creation of 2D molecular structure diagrams that make full use of the capabilities of modern display systems, using only input data expressed in file formats used for cheminformatics, is a complex task that requires a number of additional algorithms. Assuming that atom positions have been well chosen, the rendering engine is required to micromanage the precise positioning of atom labels, bonds and atom adjuncts, in such a way that the final output is correct, consistent with convention, and as pleasing to the eye as a diagram produced by a graphic designer. The techniques must be equally applicable when creating output for low-resolution screens and high resolution printed output, and make use of contemporary graphics file formats in such a way that the largest possible number of software platforms are able to display the output at any resolution without degradation or inconsistency. The main issues involved in meeting these criteria are discussed, and algorithms for satisfying them are presented.


Accessing the Chemical Identifier Resolver from Marvin

With the release of Marvin 5.12.0 users can now also access a custom web-service to extend name to structure conversion - for instance, with corporate IDs or common name dictionaries. I thought it might be useful to have a look at this new feature however I don’t have a corporate web service that I can use. This is where use of the Chemical Identifier Resolver (CIR) comes into play


Marvin 5.12.0 has been released

Marvin 5.12.0 has been released. This has an important updates for Mac OS X users, in that image to structure conversion using OSRA and text OCR for scanned documents is now supported on Mac OS X.


In addition Structure Checker configuration can be accessed via URL from MarvinSketch, Structure Checker application, and via Structure Checker API call. Users can now also access a custom web-service to extend name to structure conversion - for instance, with corporate IDs or common name dictionaries. Typing abbreviated group names is now case sensitive, When pasting unrecognised format onto the canvas, "Import as" dialog appears, and the user can choose the correct format. Structures can be copied as "Daylight SMARTS" and "ChemAxon SMARTS (CXSMARTS)" formats. The MMFF94 forcefield has been added to Generate3D and can also be used in the Conformer Plugin and Molecular Dynamics Plugin.

The complete release notes are available here


Elemental for iPad/iPhone updated

Dotmatics have announced an update to their chemical sketching application Elemental to version 1.5. No details of any changes are available.

There is a page of mobile science applications here.

Chocolat a text editor for Mac OS X, that combines native Cocoa with powerful text editing tools has been updated.

There are more text editors here.


Marvin Update

ChemAxon have just announced an update to Marvin the latest version is 5.11.5

Structures copied from ChemDraw or Accelrys Draw could not be pasted onto MarvinSketch has been fixed.


MacVector and ChemDoodle web components news

MacVector Inc have released a free version of MacVector.

If you used a temporary trial license, then when the 21 days were up, MacVector would simply refuse to start unless you entered a new valid license code. With the release of MacVector 12.7 we have changed that behavior. Now, when the trial license (or any annual license) expires, MacVector will give you the option of continuing to work, but with reduced functionality. All of the functions in the Analyze menu become disabled, but you can still open, edit, save and print MacVector documents, or save MacVector files in other formats.

ichemlabs have announced the release of ChemDoodle Web Components 5.

ChemDoodle Web Components 5 is a massive update. The most notable addition is a Full Sketcher, for drawing multiple molecules, shapes and figures, in addition to the Single Molecule Sketcher already provided. iChemLabs Cloud services and the ChemDoodle JSON format have been updated and drastically improved. The entire codebase has been reoptimized and cleaned, doubling the performance in desktop browsers and more than quadrupling the performance in mobile browsers. All Canvases now handle managing multiple molecules and shapes. Many new additions have been added and dozens of bug fixes have been implemented. We will be unrolling our new proprietary options over the next month, but of course, everything is available for free today under the GPL license!

There is a tutorial for using ChemDoodle web components here.


Using ChemBioDraw with MOE

As I mentioned in my recent review of MOE 2012 there is now support for using Marvin as an external 2D chemical drawing package, but what happens if you want to use another drawing package? Well that is where Applescript comes to the rescue, using Applescript support for shell scripts and one line of SVL (scientific vector language) we can use ChemBioDraw as the external editor. Full details of the script are here.


The Applescript section contains more tutorials, scripts and resources.


Marvin for JavaScript released

Chemaxon have just posted a link to Marvin for JavaScript on their blog. This live JavaScript implementation is a light-weight chemical editor suitable for generating basic chemical structures and queries on modern web browser pages.

They are looking for input to prioritise future developments.

There are more chemical editors here.


Deprecation of ChemWriter Structure Paste Via Java Plugin

Serious problems with the security of the java browser plugin, together with a series of ongoing (and unresolved) stability issues mean that this developer is looking elsewhere.

Given the nature of the newly-disclosed Java Plugin security exploits and ongoing stability issues, ChemWriter’s clipboard paste functionality will likely be removed altogether in a future release. Those currently using this feature are encouraged to find an alternative.


A review of ChemDoodle 5

I’ve just completed a review of ChemDoodle 5, this is a very good upgrade that focuses on improving workflow, but also adds several really useful new features.

There is a collection of software reviews here.


Marvin Updated

Marvin from ChemAxon has been updated to version 5.11

New features and improvements

  • Image I/O
    • Recently added rendering options are now available to be set from MolPrinter API (Absolute label visibility, Peptide display type, R-group visibility, Any bond style, Lone pair rendering style, Charge rendering style). Documentation
  • MSketch GUI
  • MSketch applet
  • Graphical object handling
    • When an MMidPoint object was set as an end point for an MPolyLine, getting the MMidPoint location caused a StackOverFlowError.
  • Import/Export
    • Document to Structure (d2s)
      • Names broken over two lines with a hyphen (-) are now recognized.
      • Names followed by a superscript text, for instance, a reference or footnote number (e.g., "aspirin11") are now recognized.
    • Name to Structure (n2s)
      • In some cases, such as "4-methylthiophenylmethyl", there is an ambiguity whether "thiophenyl" refers to a compound derived from thiophene or thiophenol. Name to Structure now gives priority to the thiophenol related compound interpretation; though, "thiophenyl" by itself will still be supported as thiophene derivatives.
  • Painting
    • If R-group visibility was turned off and any of the bonds had label(s) to paint, an ArrayIndexOutOfBounds exception was thrown.
  • Image I/O
    • Display parameters of charge, lone pair, peptide could not be set for molexporter. The default values were charge "in a circle", lone pair "as line", peptide "three letter format". Image copy also used these values.
  • Import/Export
    • MOL, SDF, RXN, RDF
      • Aliphatic query properties of atoms with query string were not read from MDL formats.
      • After importing Extended MOL files that contain superatom S-groups the orientation of S-groups could be changed.
      • Atom containing both aliphatic and unsaturated query properties were exported incorrectly to MDL formats.
      • SDF import returned structure with incorrect S-group embedding.
      • SMILES T* option did not export all SDF fields, but only those which appeared in the first molecule.
  • Molecule Representation
    • S-groups
      • Two superatom S-groups being each others' parents caused infinite loop. In these cases, now java.lang.IllegalStateException is thrown.
    • Valence Check
  • Stereochemistry
    • Cloning of BicyclostereoDescriptor in RxnMolecules threw java.lang.ArrayIndexOutOfBoundException.
  • Clean 2D
    • Terminal methyl-group in phosphate-ester was cleaned incorrectly.
    • Clean2D could not handle condensed adamantane derivatives. Forum topic
  • Calculations
    • Other (HBDA, Huckel Analysis, ...)
      • The --pH command line option did not work in hydrogen bond acceptor-donor calculation.
  • Structure Checker
    • If fixer action was not defined, default fixer was not applied in structurechecker command line tool.


ChemDoodle 5 is now available

ChemDoodle 5 includes significant new features and improvements, including:

  1. Round-trip editing on Windows via OLE. (Round-trip editing is already provided on Mac OS X)
  2. Round-trip editing on Linux!
  3. A revamped shape system for much easier and more precise manipulation of shapes, especially in crowded figures. Also a new quick colors button to now quickly change colours of objects.
  4. Bezier curves for complex shapes and mechanisms.
  5. Fragmentation tools.
  6. More functions for handling chemical data on the clipboard.
  7. File chooser previews.
  8. 77 new glassware templates!
  9. Hundreds of other features and improvements.

Upgrade pricing options are available.


Open Eventory has been updated

Open Eventory has been updated

2012-09-28: - updated Ketcher molecular structure editor, now also supports reaction equations - added DrugBank for structure-to-CAS and substance data search - fixed a bug that prevented merging of literature datasets - advert in navigation panel no longer covers functionality on smaller screens - added SDF export (experimental) - import of existing substance data is now possible (if you have data not within the online catalogs)

Open enventory is an integrated laboratory journal with a literature database and inventory program.


A Quick Review of ChemBioDraw 13

This version of ChemBioDraw released in August 2012 is the first release since Cambridgesoft became part of Perkin-Elmer and there are a significant number of changes. This is the first version to be released since the introduction of Mac OS X 10.7 and 10.8 and both are now officially supported. In addition the ChemDraw plugin is now supported in 64 bit mode and Microsoft Office 2011 is supported. I’ve written a brief review here.


Avogadro Updated

Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Windows, Linux and Mac OS X. The source code source is available under the GNU GPLv2.

This release highlights a great deal of new features, including a built-in crystal library, crystallographic editing, building slabs / surfaces with arbitrary Miller planes, support for Abinit (and soon Quantum Espresso), searching for IUPAC names in PubChem, custom atomic colors and radii, and much more.

See the Release Notes:

What does Avogadro do?

  • An intuitive "builder," including common fragments, downloading directly from PDB or PubChem, and peptide sequences
  • Innovative "auto-optimize" tool which allows you to continue to build and modify, during molecular mechanics optimization
  • Interfaces to many common computational packages
  • Designed to help both educational users and advanced research
  • Plugins that allow Avogadro to be extended and customized
  • Well defined public API, library and Python bindings for development
  • Embedded Python interpreter
  • Translations available in 19+ languages

For more information:


ChemDoodle mobile updated

ChemDoodle mobile has just been updated

ChemDoodle Mobile is a calculator for drawn organic structures. There are four main windows: Draw, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The Calculate page calculates properties and the Spectra page simulates NMR spectra. All spectra are interactive. The Help page contains a detailed help guide.

Calculations 1. Molecular Formula 2. Molecular Mass 3. Monoisotopic Mass 4. Degree of Unsaturation 5. Hydrogen Bond Acceptors 6. Hydrogen Bond Donors 7. Average Molecular Polarizability 8. Molar Refractivity 9. Polar Surface Area 10. logP Spectra 1. Mass Parent Peak (Isotopic Distribution) 2. 1H NMR 3. 13C NMR

There are more apps on the mobile science page


Elemental for iPad 1.0

Elemental is the Dotmatics chemistry sketch utility provided at no charge

What's New in Version 1.0

  • Copy image to Camera Roll
  • Copy Image to Clipboard
  • File association (tap and hold to load in Elemental)

There is a listing of science apps for iOS here and a comparison of drawing packages here.


ChemDoodle web components updated

I just noticed ChemDoodle web components have been updated

This significant update improves performance and graphics for both 2D and 3D components. PDB file reading has been optimized on the Javascript side, and you can now control the resolution of protein and nucleic meshes, leading to significantly faster loading. Two new spectrum components have been added, OverlayCanvas which draws several spectra in the same domain, and SeekerCanvas which shows plot coordinate information.

You might want to have a look at this review and this tutorial


JSDraw 1.3.6 Release 

JSDraw™ is a chemical structure editor/viewer built in 100% Javascript, running on all platforms, including Windows, Mac, Linux, iPad/iPhone, Android tablets/phones and Chromebooks. JSDraw 1.3.6 release includes following improvements and changes: 1. Supporting superatoms: Boc, Me, Et, Bu, Ph, COOH, CHO.  And developers are able to use custom superatom table. To download JSDraw:



Adding drop shadows to chemical structures

As part of my day job I maintain Drug Discovery Resources a website intended to act as a resource for scientists undertaking drug discovery. One part of the site has a section on bioisosteres including many examples in which the chemical structures are shown with dropped shadows.

I use ChemBioDraw to draw the structures and then save as PNG files with a transparent background. The structures are then dropped onto webpages created using RapidWeaver, within RapidWeaver there is an option to add dropped shadows to images. I was recently asked whether there was any other way to create the same effect and Matt at macosxtips suggested using ImageMagick. This applescript droplet allows you to do so by simply dropping the file.


Xemistry Web Sketcher Update

Version 3.0 of the javascript chemical drawing package Xemistry Web Sketcher has been released.


This joins a list of javascript powered chemical drawing tools. It seems pretty fully featured but I have to confess I prefer a rather more minimalist interface with templates, elements available from menus. However drawing packages are very much a personal preference.


Elemental for iPad

Elemental from Dotmatics a Chemistry Sketch Utility

Elemental is the Dotmatics chemistry sketch utility provided at no charge within many Dotmatics products. Now provided as a FREE app on the iTunes store.


There is a list of mobile science apps here.


Mobile Molecular Datasheet has been updated

The Mobile Molecular DataSheet (MMDS) has been updated. Two major usability enhancements:

(1) Additional tool banks on the left and right side of the sketcher provide simplified drawing tools that are more familiar to users of desktop chemical drawing software.

(2) A tooltip system provides tips, live demonstrations and links to documentation.


Scripting the Chemical Identifier Resolver Updated

I was reminded that whilst scripting menu items was the traditional way of controlling ChemDraw the more recent releases allow control by scripting commands. This is a major advance since menus can change or be translated into other languages. I’ve thus updated the script.

I was asked if it would be possible to do the same thing for other drawing packages such as MarvinSketch?

The answer is yes but because MarvinSketch does not have applescript support we have to do it slightly differently. Rather than using scripting commands we script system events to evoke the “Paste” command.

Full details of the script are here


ChemVector and ChemCore

I’ve added two new applications from Metamolecular to the alphabetical listing.

ChemVector™ offers a modern solution to the chemical structure imaging problem. Features

  • 100% JavaScript. No browser plugins are necessary.
  • Runs with all commonly-used browsers on Windows, Linux, Mac, and iPad. This includes Internet Explorer 6-9 in addition to Firefox, Google Chrome, and Safari.
  • Renders structures directly from individual molfiles on a server, or as inline content.
  • Renders chemical structure content directly from ChemDraw™ binary files (.cdx).
  • Declarative syntax replaces <img> tags with analogous <object> tags, making it easy for both developers and designers to work with the resulting markup.
  • Non-blocking implementation makes it possible to render dozens of structures on a single page while maintaining UI responsiveness.
  • Structures can be magnified pre- or post-rendering with no pixelation.

ChemCore is the chemiformatics foundation of all of the Metamolecular products and services. Written in Java and cross-compilable to a number of target runtimes and platforms, ChemCore is both fast and flexible.


  • Fast subgraph matching
  • Powerful graph query capabilities
  • Flexible, efficient graph traversals
  • Fast file input/output
  • A complete system of atomic weights and elemental properties
  • Sensible handling of implicit hydrogens
  • Molecule validation and correctness-checking
  • Molecule transformations, including canonicalization and salt-stripping
  • 100% Java cross-compilable to JavaScript and other target runtimes and platforms
  • Extensively tested and documented


MolPrime added to mobile science page

MolPrime is a chemical structure drawing tool based on the unique sketcher from the Mobile Molecular DataSheet

Added to the Mobile Science Page.


Chemical Drawing Packages compared

Chemical Drawing Programs – The Comparison of Accelrys (Symyx) Draw, ChemDraw, DrawIt, ACD/ChemSketch, ChemDoodle and Chemistry 4-D Draw

There is also a comparison of six chemical drawing packages here


Protein Ribbons display tutorial

I’ve corrected the broken links in the Protein Ribbon Models of Proteins tutorial using the ChemDoodle Web Components.

There are more tutorials here and a selection of software reviews here.


JSDraw updated

JSDraw™ is a chemical structure editor/viewer built in 100% Javascript, running on all platforms, including Windows, Mac, Linux, iPad/iPhone, Android tablets/phones and Chromebooks. JSDraw 1.3.0 release includes following improvements and changes:

  1. The js file is renamed to Scilligence.JSDraw.js
  2. Speeded up JSDraw on IE 6/7/8 by adopting Silverlight
  3. Added fragment-selecting tool ( )
  4. Improved drawing performance
  5. Being able to expand Amino Acid using right click menu ( )
  6. Bug: atom labels overlaps bonds
  7. Added Bracket object to support polymers ( )
  8. Added Lasso selecting tool ( )
  9. Widely supporting SGroup ( )
  10. Being able to Set object colors


CLiDE Updated

CLiDE is a chemistry intelligent equivalent of Optical Character Recognition (OCR) software. Just as an OCR can recognize characters from a scanned images of printed text, CLiDE can recognize structures, reactions and text from scanned images of printed chemistry literature. The software saves users hours of redrawing structures from printed material, as it transforms the 'images' into a 'real structures' that can then be input into databases.

The new and improved features of the latest release include:

  • support for Windows, MAC and Linux operating systems
  • improved structure recognition capability
  • improved error reporting
  • improved processing of document pages which contain tables, underlined text and page separator lines that touch a few letters
  • extended input format support with Word (DOC and DOCX) and HTML
  • extended export format support with CML and MRV formats
  • integrated support for ChemAxon's Marvin Sketch, Accelrys'Draw and ChemDraw editors

ChemDoodle Update

ChemDoodle 4 has been released and is now available. Included are hundreds of fixes and new features, recommended by customers. Read More...

ChemDoodle and Lion

From the ChemDoodle website

“We have finished our testing of ChemDoodle on Mac OS X Lion, and everything works as expected. ChemDoodle will continue to work for you on your mac, even after you update to Mac OS X Lion.
We regard Mac OS X as a primary platform and will always support it. With ChemDoodle, you can be confident that your work will be unimpeded by major OS updates.”

Chemical Drawing

More javascript based chemical drawing packages

A comparison of 6 chemical drawing packages

A comparison of the 6 chemical drawing packages available on ChemSpider Read More...

ChemDoodle, WebGL and Protein Ribbons

A tutorial demonstrating the use of ChemDoodle and WebGL to display ribbons on proteins. Read More...

ChemDoodle Web Components 4

This latest update to the ChemDoodle Web Components brings a host of new features Read More...

Structure searching using MMDS

Structure searching using MMDS

Marvin Updated

Marvin Updated

ChemBioDraw and round-trip editing

ChemBioDraw now does round-trip editing in Microsoft Word.

ChemDoodle and round-trip editing.

ChemDoodle now supports round-trip editing with the latest update of Microsoft Office 2011 (14.0.1). Read More...

ChemDoodle Updated

ChemDoodle 3.3 was released

ChemBioDraw 12.0.2

ChemBioDraw 12.0.2
CambridgeSoft have released an update for the Mac version of ChemBioDraw


Roundtrip editing

It looks like there is light at the end of the tunnel with regard to the issue of “round trip editing”. Read More...

ChemBioDraw Roundtrip Editing

Yet more on the continuing saga of round trip editing using ChemBioDraw. Read More...

ChemBioDraw Round Trip Ediiting

Workaround for ChemBioDraw roundtrip editing issues.


ChemDoodle Web Components have seen two major recent updates. Read More...

ChemDoodle 3.2 has been released

ChemDoodle 3.2 has been released! This upgrade is free of charge to our existing customers. Just open up ChemDoodle and follow the directions to automatically update ChemDoodle. Read More...

ChemDoodle Web Components Updated

ChemDoodle Web Components version 3.1 has been released. This open source HTML5 graphics and cheminformatics library continues to grow in popularity. Read More...

JSDraw Updated

  • JSDraw 1.1.0 is released with a new spreadsheet display.

ChemDoodle 3.0 Review

I’ve just finished a review of ChemDoodle 3.0 an impressive latest update to the Chemical Drawing package from iChemLabs. Read More...

ChemDoodle 3 Released

ChemDoodle 3 Released on Mac OS X

Chemistry on the iPad

Chemistry on the iPad.

Round Trip Editing

Poll on MacResearch on editing chemical drawings.

3D ChemDoodle Web Components

ChemDoodle Web Components 3.0, released which contain the alpha development versions of the 3D ChemDoodle Web Components. Read More...

Chemical Structures on the Web

“A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web.” Read More...

Chemene JSDraw - A Javascript Chemical Structure Editor/Viewer

Chemene JSDraw brings chemistry capabilities to your web pages. Read More...

PubChem Sketcher

The PubChem structure editor

ChemBioDraw Update

ChemBioDraw Update from CambridgeSoft.

Top MacInChem Searches

Top search terms used on MacInChem.

ChemBioDraw 12 Review

Review of ChemBioDraw 12.

Zem released

Zem molecular editor.

New Applications

Aten and SMSD added,

ChemDoodle Web Components

ChemDoodle Web Components pure javascript objects derived from ChemDoodle. Read More...

New Avogadro release

Latest update to Avogadro.

Tip for improving ChemBioDraw printing

I was sent this tip for improving the quality of printing from ChemBioDraw. Read More...

Using HotKeys in ChemBioDraw

Tips and tricks for using hotKeys in ChemBioDraw


A few updates and news snippets

Added ChemDoodle

New java-based chemical drawing package added to list of applications. Read More...

Marvin and JChem

Marvin and JChem have been updated

ChemBioDraw Updated

ChemBioDraw has been updated to support Mac OS X 10.5. Read More...

More ChemDraw issues

Problems with Word 2008 and ChemBioDraw.

Marvin Update

Marvin 5.0.1 has been released.

Marvin Updated

Marvin has just been updated, I've made a few additions to my review. Read More...

Mavin Review

I've written a review of Marvin from Chemaxon.

Chemdraw Plugin

Issues with Chemdraw plugin.

A Review of the latest version of ChemBioDraw

I've written a review of the latest version of ChemBioDraw (AKA ChemDraw) Read More...