Macs in Chemistry

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A first look atChemBioDraw 14

ChemBioDraw 14 was released recently and I thought I’d download the demo version and have a quick look at it, in particular to see if any of the bugs and problems that have dogged the previous version have been addressed.

Looking at the product page it is clear that they feel the most important new feature is the integration with SciFinder unfortunately I don’t use SciFinder so I can’t comment on how successful this integration actually is.

Have the problems been addressed?

One of the major complaints about ChemBioDraw 13 was that it regularly crashed, particularly when trying to copy and paste between application, I used the new version for several hours and I never had any problems with stability.

Roundtrip editing has been an issue that has dogged ChemBioDraw for many years as Apple changed the graphics support on the clipboard.

“on the Mac we used to have this feature which I will call Round 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 feature has been lost as applications transition from using the archaic PICT clipboard flavour to the modern and beautiful PDF clipboard flavour. There was no direct way to embed large data in Apple generated PDFs, and thus developers were left on their own to munge the format if they dared. And, with no standard or expectation of data embedding, applications did not bother to preserve the original PDF resulting in data loss”

However Starting with Mac OS X 10.7, developers will be able to embed arbitrary XML data in the PDFs they can generate with Apple's APIs. This means that in the case of chemical structures vendors can embed structural information in the meta data that can be then used to generate the chemical structure when copied back into the chemical structure drawing package. So problem solved? Unfortunately not.

ChemDraw 14 Round Trip Editing Experiments (Mac OSX 10.9.3)


From ChemDraw14 pasted into Word 2011 OK, Copied and pasted back into ChemDraw 14 OK
From ChemDraw14 pasted into Word 2011 OK, Copied and pasted back into ChemDraw 12 OK
From ChemDraw12 pasted into Word 2011 OK, Copied and pasted back into ChemDraw 14 OK

From ChemDraw14 pasted into Pages 5.2 OK, Copied and pasted back into ChemDraw 14 Black box
From ChemDraw14 pasted into Pages 4.3 OK, Copied and pasted back into ChemDraw 14 Image but not editable
From ChemDraw12 pasted into Pages 4.3 OK, Copied and pasted back into ChemDraw 12 Image but not editable

From ChemDraw14 pasted into Excel 2011 OK (images are not linked to a particular cell), Copied and pasted back into ChemDraw 14 OK

From ChemDraw14 pasted into Numbers 2.3 as image, Can’t copy and paste back into ChemDraw 14
From ChemDraw12 pasted into Numbers 3.2 as image, Can’t copy and paste back into ChemDraw 12

From ChemDraw14 pasted into Powerpoint 2011 OK, Copied and pasted back into ChemDraw 14 OK
From ChemDraw14 pasted into Powerpoint 2011 OK, Copied and pasted back into ChemDraw 12 OK
From ChemDraw12 pasted into Powerpoint 2011 OK, Copied and pasted back into ChemDraw 14 OK

From ChemDraw14 pasted into Keynote 6.2 OK, Copied and pasted back into ChemDraw 14 Black box
From ChemDraw14 pasted into Keynote 5.3 OK, Copied and pasted back into ChemDraw 14 OK

From ChemDraw 14 pasted into FileMaker Pro 12 (Container Field) OK, Copied and pasted back into ChemDraw 14 OK
From ChemDraw 14 pasted into FileMaker Pro 12 (Container Field) OK, Copied and pasted back into ChemDraw 12 OK
From ChemDraw 12 pasted into FileMaker Pro 12 (Container Field) OK, Copied and pasted back into ChemDraw 14 OK


From ChemDraw14 pasted into Word 2011 OK, Copied and pasted into Marvin OK
From Marvin pasted into Word 2011 OK, Copied and pasted back into ChemDraw 14 Image but not editable

So I’m afraid we still have a mixed bag of results, there may be work arounds and please describe them in the comments if you come across solutions.

The other major complaint, first filed in 2012 was the lack of support for the retina display in Mac laptops, unfortunately it seems this has not been resolved, the latest comment on the support forum sums it up nicely

I want to state that this is NOT about fancyness and eyecandy. It's about absolutely uncomfortable visual usability and non-professional efforts. I am very disappointed.

I’ve also been sent some other comments,

Have you tried using the Chemical Symbols palette tool to draw curly arrows? Electron Pushing Tool I find they seldom go in the correct place! e.g. aldol reaction, simple Diels-Alder reaction. This was one of the significant bugs I found in v13 that was ignored.

I did a little testing and I could get the arrows to go in the correct place but it did require some experimentation with different arrows, and took me much longer than I would have expected.

Where do I put applescripts in ChemDraw 13?

Several folders have been moved around over the last few versions of ChemBioDraw, most of the additional files are now stored in your documents folder as shown below. To access scripts from within ChemBioDraw you need to put the applescripts in a folder called “Scripts” within the ChemBioDraw folder in your user “Documents” folder/

cdscriptsFolder

You should than find the Scripts menu available between “Search” and “Window”.

cdMenu

This is completely different to ChemDraw 12 where scripts were stored in /username/Library/Application Support/CambridgeSoft/CS ChemOffice 2010/ChemDraw Items.

New Features

Copy and paste CDXML and molfile text to and from the clipboard for data exchange with other applications that can consume these file formats, I did some limited testing


From ChemDraw14 pasted into Marvin OK
From Marvin pasted into ChemDraw 14 OK

Unfortunately the new pKa, LogP and LogS functionality provided by Mol. Networks is Windows only so I could not evaluate it.

For biologists the Biopolymer toolbar with disulfide and lactam bridges, beta and D-amino acids, DNA, RNA, protecting groups and linkers has been updated and you can now paste peptide, DNA and RNA sequences and have them interpreted chemically with sequence wrapping and shaping.

Last Update 28 May 2014