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.

Comments

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.

Comments

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.

xmds


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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.

xmds_snap02_w350_h369

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.


Comments

Nature Style guide for chemical structures

 

Nature have provided a style guide for drawing chemical structures

https://www.nature.com/authors/guides/ChemStructureGuide.pdf

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.

style


Comments

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.

Comments

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.

cwc8-1024x931

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 https://web.chemdoodle.com/installation/changelog/.


Comments

SketchEl 2

 

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

sketchel2_snap

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 https://github.com/aclarkxyz/web_sketchel2


Comments

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!


Comments

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

and

Chemical Sketchers for iOS


Comments

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.


Comments

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


Comments

SketchEl2 Chemical Sketcher

 

A new chemical drawing app SketchEl2 has been released.

sketchel2

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.


Comments

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 osra.sf.net

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.


Comments

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.


Comments

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.

OS

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

RAM

  • 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.


Comments

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.

Additions

  • 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.

Fixes

  • 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.

Comments

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 www.chemdoodle.com, 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.
Fixes

  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.



Comments

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.


Comments

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.
Comments

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.

Comments

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.

Update

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.

Comments

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.

Comments

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.

Comments

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:

Comments

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: http://www.chemdoodle.com/buy-now

There is a review of ChemDoodle here.

Comments

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.

Comments

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.



Comments

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.

Comments

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

Comments

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.


Comments

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.


Comments

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.

Comments

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.

Comments

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

Comments

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

Comments

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?

Comments

Marvin updated

 

Marvin has been updated to version 6.2.1

Comments

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
Comments

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.

Comments

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.

Comments

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

Comments

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.

Comments

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.

chemdoodle6

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

Comments

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

Comments

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.

temp22

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.

Comments

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.

Comments

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.

Bugfixes

  • 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.
  • MOL, SDF, RXN, RDF
  • 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.
  • CDX/CDXML
  • 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.
Comments

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