As many know I wrote a GUI for the opensource cheminformatic toolkit Openbabel called iBabel. One of the options is to use the java applet Marvin for structure display and editing. A couple of people have asked me about the availablity of Marvin from ChemAxon so I thought I’d mention they also have a suite of java-based cheminfomatics tools that all function on the Mac. A number of the tools are free for limited or academic use and they have a pretty comprehensive set of demos on their website full details of which are here.

After reading the news about ChamAxon, I downloaded their suite of free programs (MarvinSketch, MarvinSpace and MarvinView). I fell in love with them. They are probably better than ChemDraw and I hope that they can remain available and updated forever. There are two things that dissapoint me, however. First: when I copy a picture to export into another application, I get a non-scalable picture. This happens with ChemDraw too and with who knows how many other application. Marvin has an excuse (it’s a Java, cross-platform, application). From what understand ChemDraw is only apparently ported to Mac OS X: it’s still based on QuickDraw, not on Quartz (correct me if I’m wrong). In practice, if you want to use ChemDraw (and other programs…), it’s more convenient if you OS 9.
The second thing that bugs me is: why nobody complains? Have you find some work-around? Has anybody found an application that reads .mol files (and .cdx, etc…) and renders them in Quartz Security?
The problem is not limited to Chemistry, nor to Science, but quite general. Up to system 9, all applications exported their pictures into a common format (‘PICT’). Today, to be good citizens of OS X, they should all export into the new standard format (“com.adobe.pdf”), but often they don’t. It’s possible, of course, to paste a PICT into an Quartz application, and even to scale it up, but you lose all the advantages of PDF.
What I mean with “advantages” is the possibility to copy a picture from application A into the application B; then copy a larger picture from B (with the picture from A embedded) and paste it into C, then into D, E… and eventually print the whole work without losing the quality (resolution).

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