Now working in Uppsala makes Bioclipse my default life sciences platform, and I'll be porting older Bioclipse1 plugins to Bioclipse2, which has a much better architecture.Bioclipse2 does not have a native Jmol Console, but script commands can easily be run with jmol.run() (written by Jonathan). I wonder if it would be hard to have a JmolScript view like this JavaScript Console... The outline on the right (written by Ola) allows me to navigate the Jmol data model.
Adding jmol console shouldn't be too complicated and probably a good idea too. It seems to me as jmol is a powerful tool that Bioclipse 2 could do much more cool stuff with.
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